From what you are saying, you agree we can treat as “halachicly true” (love that term) what Chazal said, even if it has emperically proven to be false. For example the famous “lice” case, where we “know” the opposite of what Chazal said (lice grow from nothing): We either re-interpet Chazal to conform with known facts, or are Machmir as such (since it is well known Chazal did speak in allegory) while considering the other side as well.
Rav Breil, the Rebbi of the Pachad Yiztchok, teaches us that we do not even entertain the possibility of a statement in Chazal not coming from the Torah. This we see from Rav Briel’s answer to the Pachad Yiztchok’s question regarding the killing of lice on Shabbos. The Gemora permits it, based on a scientific fact. The Pachad Yiztchok asked his Rebbi that due to the possibility that this scientific fact is incorrect, perhaps we should be machmir and not kill lice on Shabbos, just in case.