I'm not talking about API compatibility so much, but I think I read somewhere that you need to get a license even if you use a custom server. So all the custom server gives you is it decouples you from the main service.

Do you get TOTP support and Organizations on your custom server for free?

EDIT: I just tried it, and yes, you do get (at least) TOTP support for free. Haven't tried orgs, but I'm going to convert it for Dokku now and host it somewhere as a backup plan.