Torah, morality and science

The Rabbi's method, as far as I've read (and I've read a little), is that the hidden relationship between science and religion is mostly a mistake, as these are two parallel fields that for the most part do not conflict. Science deals with facts, while religion deals with religious norms.
For example, the Torah does not command us to return a lost thing, and yet the moral norm commands us to return a lost thing, and there is no contradiction here. At most, there is a practical conflict here about how to behave in practice, but there is no contradiction here.
From what I understand, it follows that the Torah's commandment does not have any moral statement or theory. For example, what the Torah permits a woman of good looks is a religious prohibition, while according to morality it is still forbidden, and therefore in such a situation it would be forbidden to do so.
I remember that Chaim Navon in Gesher Bnot Yaakov wrote, on the contrary, that from all the laws of the Torah emerges some moral thought and theory that conflicts with Western theory, and therefore we should only listen to what is written in the Torah.
As I understand it, the rabbi disagrees with his statement, right? Can we say that the point of the debate is in the identification between the Torah and morality according to the method of Chaim Navon (following Rabbi Kook?) and the non-identification according to the method of the rabbi (following Leibowitz?)
Another small point, are all the mitzvot like this according to the rabbi or are there some that are identified with some moral or ideological idea that conflicts with our theories, and so what do we do?