Just speculating here, but this doesn't exactly sound like it was blessed by Twitter: "Bootstrap will remain a Twitter project on GitHub for the time being, but we've realized the project has grown beyond us and the Twitter brand."
If this was something Twitter believed too, I imagine there would be some fanfare around this, Twitter helping FLOSS and all that.
You have to take a pragmatic perspective here as well. I'd wager that the only reason Bootstrap is a Twitter project to begin with is because of the assignment clause of most employment agreements: If you develop something at a company, the company owns it.
I can't imagine any managers at Twitter were sitting there thinking "Hey, I have this great idea that will make us boatloads of money! Let's release an open-source html/css/js framework that makes it super easy for anyone to make a site that looks like Twitter."
In all likelihood, it was a project that the developers wrote for internal ops and later attempted (and succeeded) to open source. If you look at the Impact Graph on github (https://github.com/twitter/bootstrap/graphs/impact), you can see that it's pretty much Jacob and Mark's project.
From Twitter's perspective, they can either let Jacob and Mark continue to run with it at no real cost to themselves (since it's open source and they can still use Bootstrap), or they can try to find someone within the organization to continue to maintain it, which has a very real cost -- developer time. Given that they may not find someone to fill that role and that forcing someone into it would probably be bad for the project, I think the decision makes a lot of sense for Twitter.
It sounds to me like the two guys left twitter and have decided to continue work on bootstrap. Being open source is there a reason they can't? I don't know much regarding the rules of open source but is it possible they could just fork it and continue where they left off (without twitters blessing)?