Maybe "secret sauce" is the wrong term. People ended up choosing GitHub purely because of network effects, I think. But those features are the "lock-in" preventing individual projects from easily migrating away.
If Git repos just "had" wikis, issues, etc. inside them, the lock-in wouldn't be there, so people would be switching between Git hosts all the time—and there wouldn't really be much value in a "git host" at all, beyond what just having a Git dir on your own server, plus a native-GUI Git client supporting the wiki/issues/etc. features, would get you.
Maybe there’s no secret sauce of any value and it’s just pointless github is closed source, like a form of DRM just being used against us cause we’re silly and let it be so even as we aspire to see open source flourish...