Do we really think that on their flagship phone, they're going to remove TouchID and thus the possibility of Apple Pay? I can't see it making sense for them.
Also, having just tested, this completely blocks thumb usage - there's just no way it can be done!
As for the thumb, just flip your phone over. Although this would suck if you need any visual feedback, obviously.
Yeah but you != me. And I am by no means the least dextrous person I know.
Other rumours include touchID embedded in the glass and/or other forms of biometric authentication (visible+IR cameras and facial detection being the leading contender)