Yeah, all the time. I have like 15-20 Ibanez and I'm always jacking around with neck swaps. Few are stock and I buy necks on e-bay sometimes, too. There's always some fitting differences, and on some guitars, it's caused me not to make the switch, because I realize I'd have to do too much.
Most of the time, I will re-route the neck pocket anyway, because I like to recess it, and put a little neck angle in it. That way the neck sits a little lower and the bridge is the same or higher, giving more pullup. Most of my older Ibanez guitars had neck shims in there from the factory. So I pull the shim and route an angle right into the pocket. If I'm doing that, I'll use the router to widen the pocket if necessary. If not, then sometimes I'll use a dremel, a file, a sanding block, a razor blade, or whatever.
An RG neck pocket is deep enough, so you can just widen the slot. You should take an equal amount off each side, but sometimes one side is clearly the main offender. You're really not going to know which side. You have to check the alignment, and the screw locations vs. the holes. I would take equal amounts off until it goes in. If you do it with a router only, be careful for chips around the edge. I will almost always do the "entry" areas by hand.