> If the triune brain model was completely false (as stated by the caricature of "brain is not an onion with a tiny reptile"), it would not be straightforward to even identify the neocortex -- how do you know it is 'neo', what is it a 'neo' of and so on?

This is a sort of proof-by-etymology and it isn't very persuasive. We have all kinds of words that derive from misunderstandings that have stuck, even long after the original misunderstanding was resolved. The geographical equivalent of this would be to say "we call them Indians, so they must have originated from India at some point!"

It's entirely possible that as our understanding of the brain evolves, this layered-over-time model will be seen as a quaint misunderstanding, but we'll still use the original names for the sub-organs because there's no good reason to change them.