Doing domain.com.hostname.com isn't hard to do by adding a 2nd VirtualHost into your virtual_host.conf (or virtual_host2.conf) templates. I won't be adding it because it would double the number of virtualhost on systems that are already very close to topping out their filedescriptor limits.
Right now I'm leaning towards all domains in /var/www/html (as an option, off by default at first).. and back to the simple public_html link pointing to just 1 domain (option will still be there to set it to a directory if you want).
The confusion is mainly with the naming of the link.. "public_html" implies that's where the files go, but with the directory method, it's not exactly true.
The actual ~username/domain.com is "correct" in the logical sense, but would work better with a different name for public_html, so I may just undo it.
I'm in no rush to finalize any of this as I don't want to be changing it again, so I want to make sure the correct "default" solution is used.
John