The main difference is the length of the neck, G&L made the 6 bolt a little longer for some reason. If you use a 3 bolt on a 6 bolt body you'll have to move the saddles back to intonate properly. You might have to remove the saddle springs to get the E and A saddles back far enough.
There can also be other fit issues, like how deep the neck pocket is, how deep the neck heel is, and width of the pocket and heel. I've done a lot of neck swapping on G&Ls and it only works well about 50-60% of the time. I've never been successful at putting a 3 bolt on a 6 bolt in either direction (neck or body).
Here's a 1998 3 bolt next to a 2009 6 bolt, notice the extra fingerboard length after the last fret.