Yes, and that would have meant less of both the existing (and forthcoming) Season 3 AND Season 4 material. It's now obvious that the theme of S4 will be the growing Klingon storyline (as S3 focused on the Borg, etc.), and that would have diluted both seasons' thematic value.
Anyway, they didn't want to split the commentary between two episodes, so it's a moot point anyway. I mean, how many times did we all see people saying that the didn't want to pay for the full sets, but they'd gladly buy a copy of BOBW if it was released on its own? This is CBS offering a product that the consumers have literally been asking for.
But if your a fan who will actually buy the season sets, you're forced to buy a separate disc for features that should've honestly came with the season sets if you want them. I'm sorry, but The Best of Both Worlds
special features being shunted to an additional disc have left a far worse taste in my mouth than the season two debacle. It should really leave a bad taste in the mouth of all Trekkies. It feels like we got a half-completed video game and told if we want the rest we'll have to buy the DLC (which I've seen happen).