In our 90g reef, I didn't put eggcrate (aka light diffuser) under the sand / rock, as the rock sits mostly on the bottom glass. I've been leary about putting anything larger than a small burrowing goby in there, simply because I'm unsure how stable the rock work would be if a larger burrower was in there and dug multiple holes in the sand at the base of certain rocks. However, I don't think putting eggcrate down first would make me feel any better about it. The only way I'd feel comfortable with a larger burrowing critter in there would be if I cut / shaped the bottom edge of all the rocks so the literally sit flat on the glass (which is easy enough for me to do if I would have thought of it, only time consuming). To me, eggcrate is not so much about adding stability to the rockwork, but raising the rock up that little bit so entire rocks aren't completely buried in the sand.
I'm setting up a 40g reef where I will be putting eggcrate under the rock. It'll have 4" - 5" of sand on top of it. I'm only using the eggcrate to raise up the rock that 1/2", and possibly to distribute some of the weight of the rock more evenly across the bottom glass.