Seasons 1 and 3 are the only seasons with more than two discs (both have three discs, in their case), and they are the only two with flippers as such. Every other season is two discs (except Season 8, which only has one disc)
So the discs hold 6-12 episodes each? That's not ideal, but should still beat VOD for the time being. I guess the extras must have pushed S3 over to three discs, as S2 has the same number of episodes.