They could add a developer option to bypass the new restriction, but as far as I know they haven't said they'll do that, and I don't see any reason why they would. The adb bypass is probably good enough for actual developers.

Apps can certainly detect if a phone is rooted and refuse to work, like with a custom ROM. It's up to the developer what they care about, but this is not unusual. There are ways to try to trick the check into passing, but it sounds like the kind of thing that might break on any update.