I have some parts in my tank where the rock is at the very surface, and other places where it's deeper. If you plan on keeping high light corals, you need to give them space to grow up. For a 46 gallon tank like yours, I'd just focus on making the rockwork look pretty and not worry too much about the space left at the top. Very few fish utilize the upper portion of the water column. Most prefer to stay at the bottom or alongside the rockwork, so that's not really an issue either.