In this video interview in French of Nikon France Reflex Products Chief, he says, @ the 2 min. mark, that the added thickness of the sensor cleaning module is why, amongst other reasons ("notamment"), the D700 viewfinder coverage is @ 95%.
With the constraints of body size, geometry & a thicker sensor & sensor cleaning module, Nikon had to change the position & form of the D3 mirror. Bjørn Rørslett says here: "The mirror of the D700 is clearly smaller than that of D3. It is hinged within a different kind of supportive frame too that is thicker along the edges."
So a 95% viewer is part of the mix: sensor cleaning feature, body size, flash & cost. Like everything else in photography, it's a compromise & arguably not a big deal.