Doctor Who and canon are almost mutually exclusive things at this point. The BBC and the production team have gone out of their way to not codify any sort of canon for ages.

Pretty much anything can be explained by “time travel changed things” anyway.

Besides, at this point there’s so many different versions of Shada (the VHS “reconstruction,” the novelization, the Big Finish webcast with McGann, and now this animation), you can pretty much pick your poison as to which - if any - of them fits in your personal headcanon.