Howling:Cross Dimensional niggle (Curse of Black Spot)

The spaceship that occupies the same space as Capn Avery's ship is said by the Doctor to exist in an alternate dimension (with portals between the two worlds via reflections). The adventure ends with Avery taking charge of the alien ship to sustain his crew who are reliant on the medic programme for life. I assume this means Captain Avery is now living in the alternate universe with son and crew. If so, when the TARDIS dematerialised from aboard the pirate ship to be found on the alien craft, where the Doctor finds it, has it returned to the original dimension? Because in A Good Man Goes To War, Captain Avery is one of those who assist in Amy and Melody/River's rescue (time's passed, the Captain seems to have got his son free of the medic programme): is this because a) Avery's spaceship is interdimensional, b) the Doctor has transported Avery's ship or c) the action all takes place in the alternate dimension?

I'm guessing the answers simply 'a'.