I did a variety of experiments to track down heat on the board and I doubt that the increased core voltage is a big watt contributor.
The little diode hack on the back of the Quickstart board to power VDDOUT contributes a fair amount of heat (diode voltage drop * total board current). After the R199 issue, it's the hottest spot on the system.
I was able to drop the PMIC temperature about ~7C by feeding VDDOUT from a 3.3V supply instead of the diode's ~4.2V output. Since the diode was just a hack getting rid of it gives you a better idea of how custom hardware might actually perform.
Dropping the core from 1GHz to 800MHz only drops surface temps at the i.MX53 about ~3C on the package. Cutting the DDR3 clock from 400MHz to 200MHz only brought the i.MX53 temps down another ~3.5C from that. I can't see even a 20% core voltage reduction taking much more heat out than a 20% core clock rate reduction. (I ran all my tests just with the stock ubuntu image with the 3D (pinball) demo and BBB movie running simultaneously to load it down a bunch.)
From my calculations, the core is only about ~29% of the total power budget of the Quickstart board. So if they were to run the core at, say, 1.2V instead of 1.35V I can't imagine we'll see more than a ~5% reduction in total 'system' power. It'll be cooler, but I doubt by much. The power wasted in the PMIC by the diode supplying VDDOUT higher than necessary are bigger targets. Of course fixing the R199 "whoops" saves about a watt too (~20%ish of the total power consumed on the board was due to R199 being too low of value).
-Clay