While I can somewhat explain what's happening, there's not a lot of information out there about why it's happening. In your case a timer is going off that's never supposed to; the OS is set up to periodically reset that timer so it doesn't. This is a little different though, as the timer is being triggered not by elapsed time but rather by the sleep/wake transition.
You're right that the port enable failure is a vital clue, but unfortunately it's only useful for Apple; they keep that sort of information close to the vest, so for the rest of us there's no way of knowing what that port is. @flannelist may have some knowledge of the AppleMultiFunctionManager, but unless you've actually worked at Apple again they don't disclose that sort of information.
Regarding the back unit replacement, did you see the other person on Reddit who said they had the same problem that started after they did a back housing and screen replacement?