Wow phpbb does that - that's a great idea The tablenames are hardcoded but I genuinely think this'd be a good idea to do in later versions of vB3. I suggest you suggest this as a feature suggestion. I was going to suggest a way to do this in not so many lines within config.php. However I'm not sure if php's capabilities would allow this.
Basically for all those that may know I was thinking that perhaps you could write some ifs and regexp's to check the instance of where the constant is being used. For example if the follow characters until the next gap of TABLE_PREFIX was user then replace it with something. I don't know if this is possible.
as for adding db prefix to sql queries in vB code... easy nuff to do with text editor. rather find and replace by hand anyway just to make sure im not flubbin nothing.
just looking at the vB3 DB schema it could be quite a challenge figuring out what tables exactly to seperate... hmm.