I don’t understand your view. You do not hesitate (and rightly so) to abolish customs and even rabbinic enactments when their rationale no longer applies,
or even when it does apply, if they cause harm. But here, with a strange custom that has no reason to be kept nowadays and just cancels a commandment, you dismiss it with “we have no issue with it,” or with some invention that it proves some opinion, even though the reason for the custom is obvious.

I do not simply abolish enactments whose rationale no longer applies. We require another court to permit them (and according to Maimonides, one greater in wisdom and number). They can be abolished only when very specific conditions are met (if the mistake was there from the outset, or if the rationale no longer applies and will not return, and if the need is great). In my opinion, that is not the case here, even if you are right that this is the reason and that it indeed no longer applies. I am not at all sure about either point, but as I said, even if so, it is still not simple to abolish an enactment. A custom—maybe yes.
And does the rationale for blowing the shofar on Rosh Hashanah that falls on the Sabbath still apply today? And reading the Megillah and taking the lulav? And similarly tefillin on Hol HaMoed, and more.

Obviously enactments are more complicated, although even some enactments you do call to abolish—but leave that aside, I only mentioned enactments in passing. A custom whose rationale was questionable from the outset, and in any case the rationale has fallen away, and there is a loss in keeping it—why continue observing it?! If I remember correctly, a few years ago you came out very strongly against the custom of not eating legumes on Passover; there at least you can find some logic, but here you can’t.

With legumes, the problem was that it was not a custom but a concern. A custom has force, but a concern does not. Beyond that, with legumes there is serious harm that comes from this custom (it becomes a laughingstock, and dealing with it takes over the entire Passover instead of focusing on the essence).
By contrast, in our case this is a custom that shapes the law. Strictly speaking, there is no obligation to put on tzitzit (it is a conditional positive commandment), so it is not such a big problem that the custom shapes the imposition of tzitzit. There is also no harm here, and it is not even clear that this really is the reason for the custom. From all this, it seems to me that there is not sufficient reason to abolish this custom.

Of course, there is nothing at all wrong with someone wearing a large tallit from the age of mitzvah obligation, or even earlier. But to require people to abandon the custom—I do not think there is a sufficient basis for that here.