"I think of GitHub as a collaboration tool."
Well yes but git itself is the tool at the base of the pyramid you call GitHub and co. It seems you actively want git to look like all the other things you are used to and they are all walled gardens.
GitHub takes git and basically turns it back into subversion and co. Instead of all that anarchic "no repo is king" long haired hippie nonsense, you want central control 8) I do too but only within my company, so we use gitea (other git control freak enablement platforms are available).
Why not go back to basics and start with git? Just git. Add a comms channel - it can be telephone, SMS, email, Slack, semaphore or smoke signals. Then add stuff on top of the basics and see what happens.
Quite a large project works like that already. You might have heard of Linux.
Or stick with a canned effort like GitHub (I use it for some things) and accept that you get what you are given if you abrogate your options to someone else.
Yea, I keep saying: "Git doesn't need a hub."
One of the greatest features of git is that it is not reliant on a centralized repo! Why graft centralization onto a tool that doesn't want it?
The non-git features of GitHub, like actions and CI and the issue tracker and all that stuff are fine, but I'd argue don't really belong as part of your source control system. If you need that stuff, you should be able to pick and choose the tools you want to use, rather than just live with whatever GH gives you. But they really have nothing to do with git.