You are right, you can put the plug wires anywhere on the cap, as long as they are in the right order and in the right direction. A Pontiac distributor spins counter-clockwise and the firing order is: 1-8-4-3-6-5-7-2. Pointing the rotor at the #1 cylinder is for an external reference, since you can't see the darn thing with the cap on.

Why didn't someone make a clear cap the first time? Then everyone else would have copied it, and we'd never wonder if we are getting spark or if the rotor's lined up. We could almost time the motor visually.