I've tried a few ways with a homemade jig like bingham's, and I'm starting to think that the best way to drill a takedown is to clamp on the first limb to the riser, align it, and drill both holes right through the limb into the riser ona drill press. Then repeat for the second limb.
Obviously mark the locations first and everything, but the jig is PITA in my experience.
Only downside to drilling through the limb for the alignment pins is you need to fill part of the hole in the limb from the back side with a hardwood dowel, and then you need some kinda limb butt overlay to cover it up.