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