Answer

First, it is impossible to assert anything with confidence even בלי the biases you described. We have no way of knowing anything with certainty. For us, everything depends on foundational assumptions, on various conceptions, and on the human limitations we have. Anyone who claims anything on earth with certainty does not know what he is talking about (unless we are dealing with a prophet or some other exceptional person, where I have no understanding of how that works for him).
All one can hope for is probability, not certainty. But if something seems probable to you, even if it is not certain, then it seems to me there is no obstacle to adopting it. After all, even about science you can argue that we are biased and perhaps it is not true. Science is not certain. And so it is with everything on earth (including the whole claim about bias, which itself may not be true and may be produced by the biases we have).
As for the claim itself, I’ll present it in a sharper form so I can explain. We see that someone born in a religious home usually becomes religious, and in a secular home usually becomes secular. Of course this is not necessary and not absolute (and your formerly religious friend is proof of that), but there is a high correlation. Some conclude from this that faith (as well as lack of faith) has no real substance. It is programming that comes from the home and society. This is basically a pluralistic conclusion drawn from the factual correlation (which is itself a fallacy, known in philosophy as “the naturalistic fallacy,” since a normative conclusion is being drawn here from facts).
About that I would say three things: 1. It is important to understand that according to this claim, every worldview is programming, not only religiosity. So too secularism, socialism, capitalism, fascism, and anything else you like. 2. In fact, people sometimes do change their beliefs (they become religious or leave religion), so this is not really programming. 3. Even if everyone ended up exactly as they were born, the pluralistic interpretation would still not be the only possible interpretation of the correlation I described (between the home and environment and the belief of the person raised in them). There is another possible interpretation of this situation. It may be that in order to discern faith and religious commitment, cultivation is required. For example, to be a master carpenter, one has to apprentice under a carpenter, and likewise with a scientific researcher or a doctor. Does that mean the doctor does not know more than I do about medicine? He is “programmed” to be a doctor because that is what he deals with, and I do not. Clearly he thinks differently from me because of the knowledge and abilities he has acquired. That difference does not lead to a pluralistic-skeptical conclusion. The same is true of athletic or philosophical ability, which depends on training. “Religious ability” also depends on training, and if the environment and home help it, it develops; and someone who did not receive that help has a harder time developing in that direction. After all, even morality, which is considered more universal and self-evident, still requires cultivation, education, and environmental influence. Does that mean the moral person is as right as the immoral one? No. It only means that without education and cultivation it is harder to form and develop our morality. The same applies to faith and religious commitment.
This is at least as good an interpretive possibility as the pluralistic one, and according to it faith comes out as the correct path (even if not certain), while secularism is a kind of programming (or a failure to develop the religious faculty).
One could of course argue the opposite—that secularism is the correct path and religiosity is the lack of development and cultivation. But first of all, one has to understand that all these interpretations are possible, not only the pluralistic one. And beyond that, in my opinion the interpretation I suggested is more plausible, because secularism is emptiness (not that the secular person is necessarily an empty person, but secularism is empty. It is the absence of faith, nothing more). Therefore no cultivation is required here. Religiosity, by contrast, is something very nontrivial, and therefore it is reasonable that without assistance and education it would be hard to develop it (like morality).
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Questioner:
All the best
With God’s help 
Thank you very much for the length and detail,
a deep, clear, and comprehensive analysis.
Just one small point: if you can, please explain to me how this answers the fact that there are devout Christians and Muslims who cultivate their religion and believe in it; there, seemingly, it is not complete emptiness as in secularism.
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Rabbi:
I can see two principal possibilities:
1. There it really is a mistake (in my estimation). I did not say there is no programming, only that such a situation does not necessarily indicate programming. When you broaden my description and include more than two possibilities within it (assuming they all contradict one another), you get an interpretation in which one of those possibilities is correct and all the others are mistaken. The two-option model was only meant to sharpen my point, but in reality there are of course more possibilities.
2. There is truth in their approach as well, and both these and those are the words of the living God, though problematic additions have attached themselves to it (and that is also the situation with us).
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Questioner:
Okay, thank you very much,
you helped me broaden my mind on this issue.
 
Just a small remark, if I may: I am trying to understand which problematic additions the Rabbi is speaking about. If you mean enactments and customs that were added over the generations, then although they are not literally from the Torah, they certainly have an honored place in Judaism both from the standpoint of the Torah (“and you shall do according to what they instruct you”) and from a practical standpoint (to preserve the flame and the religious society). And if you mean charms, superstitions, and false conceptions, then these do not represent faithful Judaism as the great sages of the generations upheld it, and they are not considered part of acceptance of the Jewish religion at all. Therefore, in my opinion, it does not make sense to mention them in one breath together with the severe problematic additions that were added to Christianity, where they are part of the faith itself and are upheld even by its greatest believers (for example, regarding the mother of that man, who conceived from the Divine Presence). Consider this carefully.
(And I assume your intent was only to compare in the sense that there are some additions of some kind—not in quantity and not in quality.)
 
Thank you very much.
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Rabbi:
In my remarks I did not mean to equate, only to point to a similarity. But since you raised the point, in my opinion there are additions that entered the core of Jewish faith in this sense. For example, belief in individual providence, and perhaps a few other beliefs that I am not sure how well grounded they are (such as the World to Come, the coming of the Messiah, and the like). By the way, Christianity too has different and varied conceptions, and not everyone agrees on what is included and what is not (including that conception you mentioned, for which you will find something analogous among us as well with respect to the Holy One, blessed be He, and His Shekhinah).
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Questioner:
Indeed, I heard from my friends at Bar-Ilan about your views on these matters, but I never heard or read a clear statement from you about it. Still, at first glance I saw no need to delve into it, because it is clear to me that these are things they said on the basis of the tradition they received, and not out of rational analysis (only scriptural supports from the verses). And since the sages of the Talmud are trustworthy to me in transmitting the tradition truthfully and accurately, I see no reason not to rely on them in this as well.
P.S. I would be glad for your response, but I do not want to burden you with a long exchange like this; surely your time is limited, so feel free to stop here.
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Rabbi:
They are trustworthy to me as well, but I did not see in their words that this is a tradition. It is entirely possible that this is their own reasoning. And as is known, even when things are presented as tradition, sometimes that is only meant to strengthen the point (and the medieval authorities already noted this).
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Questioner:
It does not seem plausible to me that all the sages of Israel across the board would agree purely on the basis of reasoning alone about these matters that predict the future, without even one sage disagreeing about it. In my opinion, that is proof that they indeed received it by tradition that this is how it will be. 
(And even regarding the Messiah, where Hillel disagrees and holds that they already consumed him, etc., he does not disagree about the principle itself that there is supposed to be some Messiah.)     
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Rabbi:
First, the fact that something does not seem plausible does not mean it is not true. Here the tradition has turned into reasoning, and reasoning is open to discussion and dispute. After all, I too wrote that I am not sure.
Second, after the matter entered as a binding example (in people’s imagination), people thought that this was a tradition that necessarily had to be accepted.
And third, you yourself brought Rabbi Hillel, and if belief in the Messiah can fit with a view that “they already consumed him,” then why can belief in the World to Come not fit with views that it is a metaphor, or something that already was, or anything else?
And fourth, the words of the Raavad are already well known regarding the belief in corporeality (that many who were better than Maimonides believed in it), and the words of Rabbi Joseph Albo regarding Maimonides’ principles.