You've got some confusing terminology there.
It is possible to create an account, using the main domain of the hostname- I've just done it on my test server.
Ensure your DNS is correct, however and server entries match those at your DNS provider.
hostname recordshostname.domain.com A 123.123.123.123
www.hostname.domain.com CNAME hostname.domain.com (there is a bug during entry where you don't put a trailing dot)
domain recordsdomain.com A 123.123.123.123
www.domain.com CNAME domain.com
(cwp.domain.com ALIAS domain.com)
Remember to restart bind.
Note: I NEVER use cpanel/cwp aliases and ALWAYS instruct my clients to use a port number and preferably their own domain name. So you may have to use CNAME instead of ALIAS for the cwp entry.
Once all the DNS has propogated, initiate the AutoSSL for both entries - using "change" hostname and (most easily) by logging into the domain.com account and using the AutoSSL there.
Note 2: Though I find this panel much more 'pretty', don't expect it to be as stable and bug free, as uninspiring ISPconfig.