Ideally a canon would be consistent, though that need not be the case. It depends on the criteria for canonization. If a particular canon is defined as a particular author’s entire body of work, then consistency isn’t really a factor; merely authority. This is just an extrapolation of the above point, though: authority and consistency are two different concepts. One applies to canonicity; the other to continuity.

Being recognized by authority is not the same as having authority in your own right. It certainly doesn’t mean having the same authority as that which recognizes you. All it means is that the guiding authority acknowledges that you exist.

Let’s say I’ve got a comic book called “The Adventures of Smorg”; you create a spin-off of the book that I permit. That act of permission does not, in its own right, suggest that your derivative book suddenly has the same authority as mine; just that I permit it to exist. I could, if I wanted, make the statement that everything you do counts as much as my own “core” work. In absence of a definite declaration, however, It stands as a sanctioned derivative work.

As for how this pertains to Doctor Who: it does little good to insist that the novels and audios must be canonical because they are officially licensed by the BBC. All that means is that the BBC tolerates their production. Neither in turn does that mean that they must not be canonical; all it means is that being licensed means nothing in particular.

Yes, there is no official canon; not even the TV series is defined. However, in the absence of a definitive statement it’s safe to conclude by the fact of authorship that the TV show is the primary and original authority. What’s unclear is the status of any production with an authorship outside the BBC’s internal Doctor Who production office. That there is no defined canon means there are no criteria by which to assess the authority of any material outside of primary authorship. They may well be of equal authority; they may be of less or none. That the BBC’s production office is treated as the last word on the matter, and that its lack of a definite statement is triumphed as evidence, merely goes to confirm the primary and original authority of the works under that entity’s authorship.

This is not to suggest that, say, Virgin and Big Finish don’t have their own internal authority; just that this authority does not necessarily have any bearing on works outside its immediate purview without the blessing of primary authority, which originates with the primary or original author.

By the above definition, it is reasonable to question the authority of the TV movie — as it was produced by an outside entity. It, however, is one of the few instances where the BBC’s production office (in the form of Russel T. Davies) has designated primary authority upon a work outside of its own direct authorship. Davies has stated in so many words, several times, that the TV movie “counts”. Although continuity is not a determining factor on its own right, Davies has frequently referenced the narrative of the TV movie within his scripts — which, in conjunction with his unambiguous declarations, serves to illustrate its authority upon the current production. As far as authority is concerned, then, that should be the last word.

This doesn’t mean that anyone has to like or acknowledge Davies’ convictions. No one even need respect the authority of the current production team. Still, by the above definition there’s not much room to deny it.

So, in sum: canonicity is solely a question of authority; there is no designated canon; by default, then, primary and original authority rests in those works (the TV series) by the original author (the BBC production office). People are free to interpret as they will the lack of an authorial clarification on authority; furthermore, people are free (and will tend) to ignore that primary authority as they see fit. Finally, muddling this issue with the issue of consistency is counterproductive; they’re two different discussions, that occasionally cross the same territory.

Now if you want to have a discussion about continuity — which is an aspect of consistency, as pertains to narrative — this will cover most of the concerns that you raise. If you want to have a hypothetical discussion about whether any given canon should consider consistency in its definition, then there’s room for that. If you want to talk about how a hypothetical canon for Doctor Who should concern itself with consistency, that’s fine. Just, let’s be clear what we’re talking about.