It looks as if Obito is in control, why else would his face appear on the Juubi, and how he yelled "Jinchuuriki!!!".
Yes it would be a great twist, but the Juubi is simply power, no conscience. It's simply the manifestation of strife, not intelligent enough to formulate a plan. That's why it was being controlled by Obito and Madara.
Obito didn't yell Jinchuuriki...where do you see that? Naruto is the one who said "The Jinchuuriki of the ten tails". Not Obito.
This opens other question... was it really Obito who told this?
--- Lol this is too hyped. But the chapter's cliffhanger came like that XD.
I agree anything is possible. Even with Obito's Rinnegan, it just doesn't make sense how he all of a sudden absorbed the Juubi to become it's Jin. Look at what Minato had to do to make Naruto the Kyuubi's Jin, he had to do a bunch of hand signs to make a seal and altar appear, then another hand sign to actually do the sealing of the Kyuubi inside of Naruto. Obito was lying there on the Juubi's head, dying, and not moving. And then he just absorbs it? I don't know, dumb if you ask me.
The only other thing I can think of, is maybe Obito reconnected to the Juubi, the way he and Madara were connected before, with the little tethers. Maybe he created a tether out of his stomach, and since he was already lying on his stomach on the Juubi, you can't see it. If he did that, it could be a combination of your theory and Obito doing it himself. Like if he created the tether to gain what little control of the Juubi he could, he used that control to tell the Juubi to take over his body, or absorb itself into Obito. That way it would be the Juubi doing everything, but at the control of Obito.
Or it's just plot no jutsu and whatever, Obito magically did everything that needed to be done to become a Jin whilst dying on the head of the Juubi.