That sequence of events is exactly what I'd expect for a "we screwed up, but not in a way to incur any legal liability"

1. Generic answer that "yep, it's not working, here's how to fix it" 2. Updating documentation to make it better. 3. Somebody saying "what should we do about all the other customers in the same situation? can we just shut up about it?" leading to the last email.

And then... yeah, you can't directly apologize and take responsibility because that would cost you a fortune (and really, back billing is the right answer, though maybe he could in turn offer his customers a month's discount or something). Maybe Stripe could waive some fees for a while or something, but you have to have some limits on hard to use but technically correct situations.