You actually can now, but it's still in "sandbox" stage.

https://atproto.com/blog/federation-developer-sandbox

So you could take their code, tell them to screw off, and run your own instances independently of them?

Yes, but since they’re by far the largest instance right now and would prob degenerate with you, you’d need to be cool with the fact that only people on your instance and some small other ones would be able to see your posts.