TR: Look at the Chizkuni (I think by Migdal Bavel) who says they were all allegory. And R’ Bachya famously explains how the world is about 14 billion years old.
There is a very, very big difference between just admitting that we don’t understand something (that we knew all along that we never understood) and between reinterpreting Halachah. And no one is against MBP or Kapparos because of “enlightened understanding”. The Kapparos issue is that nowadays it’s not feasible to transport that many chickens without unnecessary cruelty and therefore it shouldn’t be done (major Chareidi Poskim have said this). The MBP claim is that it never was integral to the Milah and now we should abolish it if it is in fact dangerous.