So your question is actually about the choice of board?
Yes, the dual boards will tend to use more power. Sorry, that's just a fact of life when powering more silicon.
Populating it with only a single CPU is FINE, you can absolutely do that, it doesn't actually reduce the power used by the BOARD, but it totally eliminates the power from the second CPU. But it also wipes out some PCIe slots, as I said.
If you want low power, you don't have any business being in E5-land. The E3's are better at low power, and the Xeon D's are even more remarkable, and then there's the Avoton C2550/2750 stuff on the power sipping end of things.