I think you should be able to increase the wait_us delay pretty large without any noticeable negative effects. But I've also seen firmwares use 40-50 microseconds.
I haven't checked out the other branches, so I can't say for sure if there's a bugfix branch. (I'm not part of the development team, just contributing in my spare time :D )
Funnily enough, my repo is actually forked from the upstream qmk repo.
And I don't know any other keyboard with debouncing issues, so I can't help you there. :/