Would you trust clean repos that are messed up by AI?

Yes, those ones would be at least a somewhat-plausible simulation of a real scenario people care about: a once-clean codebase that was allowed to become messy by a succession of insufficiently-careful vibeslop PRs.

I'm not a huge fan of their methodology for the AI-degraded cases either (ideally one would set up the mirror pairs by taking some real repositories and rewinding history a month or so and then having a succession of independent agents reimplement each bit of feature work and bugfixes over that period of time), but it's at least a coarse approximation whereas I just don't trust the cleanup methodology to resemble anything real in the first place.

No, because the outputs will still be "in distribution" so to speak.