Regarding WHO canon, I think the only thing that 'doesn't count' are the novels and audios. Mainly because a lot of them have been adapted to the new series-the whole destruction of Gallifrey, Human Nature, Jubilee etc. and it's kind of weird to have the same events, or similar ones twice. Paul Cornell, who wrote the essay, contributed a LOT to the novel line....
But the timeline flux thing has merit. The Doctor changed things when he brought down Harriet Jones, leading "Harold Saxon" to take over. And then there's the whole year thing.
Doctor who's canon has had it's share of continuity problems over the years-the origins of the Daleks, exactly when the UNIT stories take place etc. but it's been fairly consistent otherwise.
Star Trek has had it's share of continuity issues too. The whole Klingon thing, the "United Earth space probe agency" etc.