Tonight's Doctor was in a blue bow tie.
I think that, behind the door of number 11 was a Doctor in a red bow tie, and the "do not disturb" notice was needed because it is vital at this stage that neither Amy nor Rory finds out there are two of them. It is his greatest fear, because he knows real doctor will one day destroy ganger doctor. Ganger doctor is learning about a "good death", including from the minotaur.
The red Doctor in the room is, of course, not real - just as the weeping angels were not real. Perhaps the real red Doctor is hunting baby Melody and the little girl who regenerated.
Amy and Rory had to be left, for they were searching for the Doctor at the start of the Impossible Astronaut, and we are now approaching that point again.
I agree completely with how strange Amy's comment on finding Melody was. Either there's more plot there too, or we just have to assume that being in some sort of state of suspended animation during gestation does rather interfere with the normal bonding process.