I don’t disagree with your post but I’m still unclear on how you envision gatekeeper should work.
You want the ability to choose a different “authorities” that verify and sign binaries? That makes sense to me but is unlikely to relieve any of the issues in the post.
Also what do you mean by “even yourself?” What would that option look like?
You could like, just trust a single binary. Have a button right there in the popup that already shows up.
Right next to where Apple's root CA is, you add your own.