I’m new to CF and D1 but from what I have learned, _cf_KV is an internal table used by CF to manage the serverless D1. It seems you ignore it and don’t delete it. This is why you don’t create it (it is already created when the d1 instance is initiated) and dump doesn’t dump it. Somebody might be able to answer that better.
Cloudflare supports domains of any tld through the standard services, it is only Cloudflare Registrar where the tld matters. You can use every other feature of Cloudflare without using Registrar.