The incumbent Master of the Land of Fiction is a writer of a pulp schoolboy serial (and, Miles and Wood argue, a thinly veiled Charles Hamilton, though the veil here is at least thicker than the last thinly veiled thing related to Hamilton). It's made clear that it's his creativity and ability to write that holds the thing together. So why on Earth would the Land of Fiction want to sack its writer-Master in favor of the Doctor, a character who has never displayed any particular literary ambition?
The clue is in episode two, in which Gulliver makes a comment that the Doctor is a traitor to the Land of Fiction. What on Earth could that possibly mean? (Yes, like all of Gulliver's lines, it's actually from Swift, but we are, I think, meant to assume that what he says is true, if oddly phrased) The obvious answer is that the Doctor is originally from the Land of Fiction. In fact, if we take Gulliver's line at face value (and there is admittedly some reason not to, though it seems to me given the rest of the story there's more reason to), the Doctor must hail from the Land of Fiction. You cannot be a traitor to a land you are not from.
The simplest explanation of all of this is that, on some level, the Doctor has always been a part of the Land of Fiction - intended to be its master and controller. And that he escaped. Thematically, this makes sense. Going back to Whitaker's conception of the TARDIS, if we look at how the ship is explained in An Unearthly Child, one of the most unusual things about it is that the Doctor explains the TARDIS via the metaphor of television. This recurs in The Time Meddler, where the Doctor describes some controls to Steven all of which are recognizable as television controls. And in The Chase, where what kicks off the destabilization of the narrative is the threat that the Doctor might trade in the TARDIS for watching stuff on television. Indeed, the opening credits of the show are done with a technique called howlaround that is based on exploiting and manipulating the technical limits of television signals And Miles and Wood write several times about how Troughton's Doctor often peers out of television screens, both in the story (as when he appears on a monitor in The Wheel in Space) and outside of it, when he looks at the camera itself. And when he looks out, he appears aware of what he is looking at. The sense is that the Doctor can cross the thin membrane that separates the world behind the screen from the world in front of it.
In other words, since day one the Doctor has been a character who appears to harness the basic power of television. And he has consistently used this power in order to tell stories. He appears to be someone who can create an infinite number of stories. He has, in other words, always fulfilled the role of the Master of the Land of Fiction, except instead of writing stories by sitting on the sidelines he writes them Mercurially - by throwing himself into them and creating them through his own existence in them.
In other words, months before The War Games, The Mind Robber has quietly given us an origin story for the Doctor that is almost, but not quite, what we eventually get from the later "official" version. (After all, it is not as though no writer in the first six years had a guess on where the Doctor came from. If I could dig up David Whitaker and ask him one question, in fact, it would be what he thought the Doctor's origin was.) The Doctor fled from a position of responsibility, stole a spaceship (or, in this case, storytelling medium), and ran off to have adventures. Except that instead of being a Time Lord from Gallifrey, he is the designated Master of the Land of Fiction - the writer and creator of all stories. And he's gone on the run to live the stories instead of simply writing them.
Notably, this never quite gets contradicted, even when, later in this season, this shadow theme of The Mind Robber gets done as the main plot of two episodes. Because the Land of Fiction is outside of the universe, and because the Doctor fled it into the universe, he presumably became "real" instead of just fictional. And thus he became something else that served much of the same narrative function - instead of a wanderer in the dimension of narrative, he is a wanderer in the dimension of time. The Time Lords, with their "look but don't touch" ethos and distance from the world, are a fair enough metaphor for the Land of Fiction itself. So the fact that, outside of the Land of Fiction, he is something else is hardly an issue.
Still not convinced? Read the whole thing.
What's remarkable is how consonant this theory is with Moffat-era Who. It seems the current showrunner has been thinking along similar lines.