Not really, they had to come up with a new design for the 1-disc "Planet of the Apes" (really just disc 1 of the 35th Anniversary edition) and they could have easily housed the 35th Anniversary disc in a 2-disc keepcase with very minimal changes to what's already in the set, they pretty much...
No it doesn't, there are scenes in the theatrical edition of "Battle" that were removed from the "extended" edition. You gain some footage but you lose some, too.