Nick Baker framed it as a choice, clock bump or two more CU's. Surely enforced by shortsighted bean counters. They should have done both, or even failing that at least just the CU's IMO.
Doing both would probably have blown their power budget, and they were looking into doing this far too late to do a major redesign of cooling and power supply on the board. We don't even know if enabling the two additional CUs would have required a clock drop in order to meet power and yield targets.
ROPs are the area where XBone is most behind PS4, and according to the Last Light dev these do make a difference, and the clock bump at least improved this (along with BW, triangle setup, tessellation, compute). And additional CUs with no additional memory bandwidth to feed them or write their output to a buffer would have offered diminishing returns
I'm inclined to believe the hardware guys when they say that the upclock was the best option under the circumstances.