To be clear, I wasn’t suggesting that you run your own registration server. I was just saying that you could run PageKite yourself. You’d have to run the PageKite server in the cloud somewhere.
If you want to go the full registration server route…
The api subdomain is what the gateway talks to when setting up domains and such. Every other subdomain (except for www) is available for registration. nginx is just used as a reverse proxy for the registration server, primarily because we run several other services on the same host (such as the add-on and update proxies).
The registration server serves as the DNS resolver for the full domain, so your NS records must be set up to point to it. If GoDaddy won’t let you do that, you’ll need to look at hosting your domain elsewhere.