I actually can't say I see a flaw in your theory. You see, that milk could have been Madara in disguise because he wanted to spy on Naruto and make sure things were going according to plan.
That could also have been the form he was in under the other boulder. So, Obito found the milk(Madara) and drank it, so it gave him the power to get out of the rocks and Madara's chakra infected him and turned him evil. So, Tobi could still be Obito.
