I always thought it was best to think that Jon Voight was playing the son of Peter Graves character.
That is an interesting observation about the Federation in the first of the new films. I have always thought that the Federation did not take on any great level of significance until the TNG. Sure it was mentioned in TOS but it was mostly unexplored background. Particularity because the idea was not created in the earliest episodes. Even later it would have little relevance to stories of a ship exploring the unknown.