Cost = Unlikely This is not the reason for reducing the size of the pentaprism. The saving would be miniscule compared to the cost of re-engineering the design and running a sperate component production line just for the D700. Better to use the D3's pentraprism than to have that extra hassle.
The dust removal system? = Unlikely The dust removal system shouldn't impinge on the pentaprism.
But the prize for identifying the mostly probable reason goes to MarkF.
The pop-up flash is the only reason that makes sense as to why the viewfinder area had to be shaved to 95%. The extra space needed by the popup flash requires a slightly smaller pentaprism. It's not a problem for a DX camera due to the smaller image area they cover but on an FX camera the only other solution is to make a much larger finder housing and seemingly Nikon didn't like that alternative.