I used to work for Apple. I don’t believe the missing parts story because as you said, how would that even happen. But, if any parts have been replaced, especially the home buttons / finger print reader, they will refuse to fix, and I never understand why. So that may be what happened.
Also Jobs was 100% behind this stuff. It’s so annoying when people treat him like he was some tech god. He was a twat.
The refusal is likely tied to liability, in that they see any aftermarket parts or OoW repairs as a potential failure point and fear the customer may blame them for it. It wouldn’t even matter if the quality of work or parts is as good or better. There’s also another factor of trying to oversimplify any repairs/service to allow them to eventually hire unqualified/uneducated ‘techs’ for things who don’t have a clue what’s going on.