Using the same PCB design is very common, the raspberry pi board has the same thing for its A and B models. Any rerouting of traces necessary is done with zero ohm resistors. Open up an electronic device and you often see 'optional' parts of the PCB that we're never occupied by components.
Keeps cost down due to higher numbers produced (although this hardly applies to Apple as they do only big numbers anyway) and only 1 part to keep in stock, makes perfect sense.
As Apple makes both the A6 and A7 SoCs it's easy for them to make sure the same pinout is kept. I think it's very likely now to be an A6 for this reason.
You can't compare it to a hobbyist board that has a run in the tens of thousands (or low 100k's) to a board that has a run in the ten millions in a much higher margin device. Any extra design effort is trivial at that point. For the same reason, sticking to the same pin out every generation would be needlessly prohibitive. Intel is changing at least every other generation.
I think their similarity of shape is mostly driven by common enclosure design and multiple common parts. The pin outs may be identical incidentally, especially if A7 is a swift revision, but there's no need to keep it the same to save a couple hundred man hours on board design. Packaging design and validation would actually be the much larger hit there.