Allyn Gibson wrote:
Except for in "The Daleks' Master-Plan," that is. The Doctor can control the TARDIS there.
After he steals the Monk's navigational unit. Which promptly explodes.
It's stated fairly early on that the Doctor could
steer the Tardis if he's able to program it with accurate positional data, which suggests that its onboard GPS system is broken, and he doesn't have the time/ability/data to be able to set it manually.
I think you might be right about the story arc in this comic. DWM's Ground Zero arc did something broadly similar in the 90s.