If you don't symlink the conf.php file then each of the sites can have their own base_url set in there.
symlinking the data directory seams like it would work. Hard to know without doing it then seeing what happens, then going from there. Take a step, debug, take another step. Unless someones built what you're building before the answers may be slim.
"better" is very subjective, what are you looking for? Probably you're not going to find much. Mainly because the skins in jamroom are a lot more than just a different set of colors like they are in other CMS systems. What functionality exists in the site is largely exposed because the skin decides to expose ( or not expose ) it.
If you've got an idea of what you want, talk to Nate get him to build it for you. He posted that hes available a couple of weeks ago.
profile_index.tpl is the default for when the profile loads and no tab is selected.
profile_item_index.tpl is the default for when one of the tabs (eg: audio) is selected. It usually would show a list of audio items
It was an analogy in response to "...If they are not compatible the choice ought not be there...." it was not meant to be cleaver, just an explanation as to why all things from all skins do not work everywhere.
If you need those two skins functionalities merged, he'll be able to do it.
What jamroom is is a platform for building stuff on, the skins are things that have been built. Just like you can build a boat with wood and you can build a plane with wood, that doesn't mean a wooden aircraft wing will attach to a boat, you need a builder.