The Tardis the two girls seems to have show a new(or unknown) capability. Although the chameleon-circuit, internal changeability and multi-room nature of it is know of it is know, it does something we have not seen before.* The Doctor enters the cafe through an exterior door, and later Clara exits the cafe into the control room of the Tardis. The Girls then "fly"(whatever) away and the "Cafe" fades from around the Doctor.

There are two possible explanations of this.
However the scene showing the girls Tardis in flight seem to indicate on in particular. The control room it self does not have to be the room with the exterior exit, in this case it is the "Cafe" recreation that matches the exterior "Cafe" Chameleon-disguise. The other possible explanation would be that the "Cafe" is some sort of temporary yet physical projection that is only there while the Tardis is landed. The look of it in flight however seem to indicate that the "Cafe" is now an actual room in the girls' Tardis, and that it is the one with the exterior exit in its current configuration.

Oh, I really think they need to redecorate the control room, at the very least it needs some girly colors.

*grins*
~Hypatia >i< ..:::

* Unless I missed an episode someplace, there are a lot of them.