I've wondered about this too. My best guess is - if a warranty repair is required BECAUSE you didn't do scheduled maintenance, they probably won't consider it "under warranty". But if it's an issue which is unrelated to neglect, e.g. your battery modules fail and your car no longer gets the 70% warranty range, then my assumption is that they will still cover it.
BTW, I have a model year 2019 vehicle, and have yet to take it in for maintenance. (But I also haven't had any warranty repairs needed, so I haven't needed to find out the answer to this question the hard way.)