Thanks for the insight everyone, just what I was looking for! So is a widespread area of cumulus more than a couple thousand feet thick less concerning than a smaller area that extends 1,000 feet above the rest of the cloud?
If you are on top of an undercast and it is not building, then you will usually be in the clear and smooth. This can be pretty common downwind of the Great Lakes in late spring or early summer. This "lake effect" weather is benign but often MVFR, and it's simple, safe, and comfortable to fly on top, dodging random buildups if required. (In the winter or early spring it's a massive ice machine.) And if the overcast is due to a indolent stationary front or closed low with relatively low tops, then flying in the clag for miles is not that big a deal and not that bumpy as long as there is no icing potential. I've had a few flights like that where I didn't see the ground except on departure and final approach. Nothing but gray in between. But usually it's desirable to get on top of low layers if possible to the clear sky above, or at least between layers.
If the undercast is at 9000 and building up toward you with taller buildups around and frontal activity or widespread convection, that's a whole different story. It's often safer to fly underneath this kind of weather, if practical, but often uncomfortable. It's not that much fun to get caught on top of a building cumulus layer on a hot, humid day in a light single. If the weather is going to be like that, fly early before things build out of hand. It's usually not possible to stay above the tops in a light single.
As you fly more in various weather conditions, you will gain experience about what you are comfortable flying in and around. The good news is today, in contrast to yesteryear when I earned my IR, we have much better in-flight weather awareness in the cockpit. Punching though the clag with little or no precip on the NEXRAD is one thing. If the NEXRAD weather is lighting up ahead of you or around you, it's an obvious heads-up to divert.
The questions you are asking is what I was asking my instrument instructor during IR training. We did a lot of actual IFR during training, so I answered a lot of those questions in flight with an instructor. If he wasn't too worried, I wasn't too worried, and I learned a lot about what you can fly in, and what was approaching weather I didn't want to tackle in my plane.
