If you are going to mount to a pickguard or pickup rings, you will want the plunge cuts, so that your adjustment screws won't hit the wood as you try to screw them in. By contrast, you don't want plunge cuts when you direct mount, because you are trying to get the screws to mount into the wood, and plunge cuts reduce the amount of wood for the screws to thread into.
If you want to use a pickguard or ring on a body routed for direct mounted pickups, what you could do is shorten the adjustment screws to precisely the depth of the pickup routes, so that they will be long enough to allow you to adjust the pickups to any height, but short enough to not stop up against the wood.
Alternatively, just do what I did with my scratchbuilds, and drill a hole under the adjustment screws with a drill press, to give clearance for the adjustment screws, instead of a plunge cut.
