Putting live rock in the dark is a shame, when you have so many organisms and algaes that depend on photosynthesis in order to maintain homeostasis. Putting base rock in the dark (like in filters and non-lit sumps) over time it will be colonized by bacteria and filter feeders, but will lack any photosynthetic organisms living on the surface. This does not say that base rock can't harbor bacterial and algal cysts which will bloom and grow when exposed to light.
Also, base rock and live rock are (and should be) really porous. Toxins, chemicals, and even phosphate can leach into live rock over time. When phosphate is leached into a rock over a period of time and then put into clean water, there will be massive algal growth on the rock because of the phosphate in the rock is being leached out. (researched from second hand research) I can provide a link if needed. It will just take me forever to find it. )