I agree with strider. Those two different PAPs will result in actual pin-to-PAP and MB-to-PAP distances that aren't that far apart. The ball as drilled will probably be slightly earlier than the intended reaction. It wouldn't be perfect or ideal, but on a house shot it will probably work just fine anyway. On a harder shot or in a larger arsenal where you're looking for a very specific reaction, you might tell a difference. The difference will be larger for the strong asymmetric than for a weak asym or symmetric ball (using the virtual MB instead of a marked MB).
Regarding the 4 X 5 type of layout for an asymmetric ball, most people interpret the second number as being MB-to-PAP rather than CG-to-PAP when there's a marked mass bias. If your driller is ignoring the MB, get out. If the second number is indeed the MB-to-PAP, there's no problem using that layout system.
SH