I've done this before for a client and it's in use right now. It works fine, and if I recall correctly the database.table.column syntax is part of the SQL 92 standard -- all versions of MySQL should support it. Just give it a try!!
For FanHome I decided that 5 sets of identical PHP files was a waste so I cooked up my own version of co-branding and I'm using that (e.g. template / replacement var sets) on FanHome.