OK, I see what you mean. I've run into the same problem on a severely tapered wing. I think I mitigated (not solved) it by getting the ribs roughed out and then putting 1/2 inch foam spacer blocks betwen them and using a long sanding bar.
Actually your problem with stacking ribs is real, but usually ignored. The individual ribs comes out tapered in thickness from what you want to less than you want. I think you could solve this by making the root rib template the next bigger rib, rather than root rib size. That way when you sand the ribs square they would be the right size. Does that make sense?