Wow. You really think this is tied into BR's plan to re-brand all of Trek with the 2009 film?
Not specifically, no.
But Bad Robot were reported to be displeased with having their hands tied when it came to the merchandising approach to Trek.
Now the guy who actually made the VAM for STID says that the decision to split the extras was not all on Paramount.
Who else would make that call then?
I'm just making wild guesses, not trying to present anything as fact.