If that’s really the case, run another GitHub instance then. Not all tens of thousands of users need access to the same codebases. In the kind of environment described someone would want identity boundaries established around each project anyway…

Hm not really. I manage the GHES instance at my employer and we have 15k active users. We haven't needed to scale horizontally, yet.

GHES is amazingly reliable. Every outage we have ever had has been self-inflicted; either we were too cheap to give it the resources it needed to handle the amount of users who were using it, or we tried to outsmart the recommended and supported procedures by doing things in a non-supported way.

Along the way we have learned to never deviate from the supported ways to do things, and to keep user API quota as small as possible (the team which managed this service prior to my team would increase quota per user anytime anyone asked, which was a capital-M Mistake.)