[Myka]

Without any life on the base rock, it's like skipping the clear coat on your new fancy paint job - there is no protection. It leaves the rock open for all sorts of nasty cling-ons - particularly the form of nuisance algae or cyano. Even after taking care to remove any trace (or massive) phosphate from the base rock there will be phosphate and nitrate introduced to the tank as soon as the old tank is moved over and the fish and corals are eating and pooping. Once that algae starts to move in, and it usually does when you start with base rock (remember, no protection on the rock), then many of those algae will also release toxins as a form of chemical warfare to inhibit growth of real estate competitors (your coral in particular and also coralline algae). Now you have a nasty mess. The number of tanks I've seen start with base rock that have major trouble with algae and cyano in the first year hugely outnumber those that have no issues.

Try something...add a piece of base rock to your established reef in a lit area of the tank (putting it in the dark is cheating), and see what happens to it. I will bet you 9 times out of 10 that piece of base rock will get covered in nuisance algae even if the established live rock doesn't have a trace.

This is just what I've observed over the last few years when base rock has become so popular.