What kind of lights do you have? In general, I would say three inches deeper will not make a difference in your case. I will qualify that by saying that some high light corals such as SPS
can be effected by a 3 inch difference if your lighting is already on the low side.
As far as the Rock displacing water...I have no idea what the ratio is. I know you will be effected as much by volume as you will weight. For example....if you put a one pound block of lead in the tank it wouldnt displace nearly as much as a fully inflated beach ball. Hopefully someone can give you a better answer.