“PAA: You’re basically saying that the concept of nishtaneh hateva proves that any metzius Chazal used to codify a halacha can have changed since their time, thus nullifying the halacha by simply engaging in a debate whether the metzius used changed? Where do you draw the line?”
Yes it does prove that the metzius could change. You can debate the metzius on any issue in which the metzius is debatable.
“And how do you even determine what metzius Chazal used to codify a halacha and whether they in fact based it on a metzius or rather only used a metzius to explain a halacha that is in reality binding irregardless of the metzius which was only given as an explanation for a set halacha [i.e. isn’t given as a basis (causatively) but as a ta’am]? We don’t pasken based on ta’amei hamitzvos.”
Generally speaking, when the Rabanan create a halacha, decree etc. it is because of a metzius; they don’t use a metzius to explain the halacha because there had to have been a reason to create the halacha in the first place.