I'm by no means an expert but from using Coolbook (successfully), I think you're right. My understanding is this:
Coolbook has the ability to control both the CPU frequency (clock speed) and voltage (undervolting). Undervolting by itself doesn't have any performance impact (provided you do it right). In fact it will usually speed your computer up (that's been my experience) because the Air underclocks the CPU when it gets hot - undervolting helps it run cooler so it can run at higher frequencies for longer.
If you don't set up the frequency / voltage settings right though, it may be underclocking when it doesn't need to - for example if you've only set a voltage for 800 MHz, that's all it will run at. It's worth checking your coolbook settings to make sure it's using the highest frequency when under load.
But every CPU takes undervolting differently and has a different ability to tolerate lower voltages without failure. While one might benefit, another might experience problems even with minimal undervolting. Also, Intel's voltage specifications are set to a range for a chip, and Apple is going with the average specified range and not to an extreme by undervolting each chip. Since all chips vary within the range, it would be time consuming to test each chip against the range. So, a standard MBA setting will work for all chips, in theory. I would increase the voltage and see the differences. Actually, I would remove CoolBook and delete it from the trash bin!
I personally don't understand anyone using CoolBook on a rev B/C MBA with an Nvidia GPU and Penryn CPU. Surely Apple has maximized a managed environment with components working together in congruence to be efficient, while achieving certain levels of performance, thus equalling exceptional user experience. Messing with it seems counterintuitive to me.
The thing is the original MBA had a horrific graphics system compared to the Nvidia (5x worse than Nvidia). In addition, it had a higher voltage CPU than the Penryn in rev B/C MBAs. That created massive heat for the tiny system. It was too much power trying to drive terribly inferior graphics resulting in complete failure of the system in many cases even when watching a benign video simple for an iPhone (maybe exaggerating).
The point is the original MBA was terribly inferior to the Nvidia GPU versions. While CoolBook was successful in the original MBA, Apple corrected the issues requiring Cool Book in the original MBA so those issues were simply not a problem for Nvidia MBAs. The result is an already finely tuned MBA that doesn't need reduced voltage to keep heat lower as the heat is not too great in Penryn/Nvidia MBAs even when hitting the system much harder with CPU and GPU intensive tasks.
I would personally stay away from Cool Book at all costs UNLESS you own an original MBA.