So if I want to publish a project under some license and I put a comment in an AI generated file (never mind what I put in the comment), how do you go about proving which portion of that file is not protected under copyright?

If the AI code isn't copyrightable, I don't have any obligations to acknowledge it.

You're looking at this as the infringer rather than the owner. How do you as a copyright owner prove you meaningfully arranged the work when you want to enforce your copyright?

Copyright office says this has to be done case-by-case. My guess is they'd ask to see prompts and evidence of authorship.