I've seen a lot of guitar bodies with carved tops where the builders carve the top and then route cavities, drill holes etc. after building complex jigs to compensate for the carved top. What's the problem with drilling and routing everything and carving the top absolutely last? I'm at this point in construction.
They do it because the router is removing material at 90 deg from the surface of the guitar. For the pickup pockets this is less critical, but, important none the less. For the neck it becomes more critical. Also, when mounting a tune-o-matic bridge, drilling the holes for the posts becomes dependent on the body's top shape too. If you look at a les paul, prs, or any other carved top from the side you will notice that the top is thicker under the bridge than at the neck joint. This is done to deal with a predermined neck angle that they are trying to achieve. But, to route the pocket out to keep that neck angle it's advantagous to have that slope already carved into the top. Even at that point, they are still making jigs to give even more angle to the routed pocket in some instances. Like I said before, it's all predetermined in their designs. In theory, you could make jigs to route out the pockets from a flat surface that will give you the angles you want, but, what if in the process of shaping the top, you remove too much or not enough thus changing the angle you should have had. I like to carve in the slope, then route out the neck and pickup pockets. After that, I move to the edges to carve in that "dished" shape. I'm sure everyone has a way they are comfortable with. In the end, all your doing is proceeding with each step so as to not ruin anything you did before it.
if you build a guitar with a neck angle and a TOM bridge, is the TOM perpendicular to the body or to the strings?