That doesn't mean that he's not an advanced human from a future civilization or colony world. The Doctor refers to himself as a human being in "The Savages" for example, and in "The Evil of the Daleks", it's implied that the Doctor has become more than human only by virtue of his extensive time travelling. The whole Time Lord thing wasn't established until later.
That does seem to be true -- the Doctor also referenced "we humans" in "The Sensorites." And he was referred to as having a "special human brain" in "The War Machines." The Daleks in "The Chase" referred to "The Doctor and the three humans" at one point, not "the other three humans" -- but otherwise they lumped the Doctor together with "the humans" or "the four humans." As late as "The Faceless Ones," the Chameleons identify the Doctor as human, though that might just be an assumption because they found out the Doctor hadn't been substituted by one of them. And he doesn't protest being called human in "The Seeds of Death."
Then again, in "The Ice Warriors," the Second Doctor says, "What do you mean, I'm only human? As a matter of fact--" but then he's interrupted. And in "The Wheel in Space" he explains Cybermen to another character as having once been "human beings like yourself" -- implying he himself isn't one. He also refers to humans as "they" in "The Enemy of the World."
Still, how is it relevant? It may be true that the makers of the Cushing movies had no reason not to make the Doctor human at the time. But it is also true that the Doctor has been defined as an alien for the past 44 years at least, so there's still no way to reconcile the movies with the series continuity as it now stands.
And even at the time, the continuities were clearly different, since he wasn't a person who came from another world and another time and was known only as the Doctor, but was a present-day English inventor named Dr. Who.
And really, what's wrong with that? It's all make-believe anyway, so where's the harm in doing different, incompatible interpretations of a fictional premise?