Well, check the price for the 6-disc season 3. I doubt you'll see a difference.
You got me!
In the UK, one of the TOS-R sets is a bit cheaper than the other two so that it becomes maginally more economic to buy the complete box set. Strangely enough, I think the cheaper set is season 1 (7 discs) while season 2 (6 discs) is £5 more expensive.
Also, season 2 of TNG on DVD was never any cheaper than the other seasons for being one less disc.