Gigabyte had problems in India with humidity entering between layers of the pcb (mb pcs have 6-10 layers or more) and causing shorts. They had to use fiber glass woven in another pattern to slow down the speed of humidity penetration and reduce the number of boards returned.
With Haswell it may be the case that more integration and the lower heat dissipated by the cpu makes them able to reduce the number of layers on the board which results into thinner boards.
It may be a move on their part save a couple of dollars on pcb reducing the layers by spending half a dollar or less for conformal coating which would make the board more resistant to flexing.
Also, since Haswell has much lower power modes (using little power on idle), the coating may help with reducing emi coming from video cards and the VRMs.
Anyway, just guesses.