Can you refer me to where you see that you need a unique ID? The terms “sub-domain instance” and “Netlify instance” are not terms that we use in the documentation.
To me, it seems like you’re trying to create multiple sites. The IDs are randomly generated and can’t be manually set. There is a name for the site, which you can see in the UI and in the API, and you can set a custom domain (top-level or subdomain) for it if you also create the appropriate DNS records. Both the UI and the API support setting the custom domain of a site.