Layout definitely matters! Surface also matters. Specifically when you're trying to attack a specific condition, layouts matter as well. I know a few PBA bowlers who just put the same favorite layout on all their balls and then adjust according to how the balls themselves differentiate themselves.
However, knowing your PAP and then knowing what layout gives you what result down lane is very important. If I have a very dynamic ball that gives a lot of motion due to the core/cover combination, I'm gonna put longer Pin to PAP layout on it, so it's controllable for me. I'm kind of a stroker. I throw between 12.5-13.5mph but I'm fairly accurate. I'm also rev dominant.
On my dry lane pieces I go with standard leverage layouts so I can be sure to get the ten pin out. There's nothing more frustrating than getting to the pocket continually only to see a ring ten pin all day long. That's an indication that your ball is coming off the spot too hard and needs to be more gradually slowed down. This can be done with surface; moving into the oil a little more or having a weaker layout. The object for me is always to get that damn ten pin out, since I'm right-handed.
By changing layouts on my balls they become more useful in tournament play and there's fewer chances of me labeling the ball as a dud.
Lately I have been able to use medium oil pieces that I drilled extremely strong, on heavier oil patterns with success. So yes,.......layouts matter immensely.