Throughout the moodle core there is use of $CFG->themedir and $CFG->themewww, but these variables are not used in some places, thus making them useful.
I've produced a patch which fixes the few places where these variables aren't used (and copious bits in the standard themes).
Mostly its just replacing $CFG->dirroot . 'theme/' with the themedir variable.
In order to keep previous behaviour I added $CFG->httpsthemewww to keep places happy which used httpswwwroot.
Also in get_list_of_plugins I added a case statement which allows the themedir to be taken notice of.
These changes mean that a completely different theme directory can be used and is taken notice of - the theme selector works too.
Obviously theme authors would need to use these variables - and i've patched the stock themes, but this does mean that the variables are useable.
We wish to use this to allow the core and themes to be kept seperate on a shared hosting solution.