This is what I’ve heard as well, though only applying to the biomechanical characters. So, the Toa in the movies are ‘more canon’ (excluding inconsistencies like the Hordika weapons), but the Vahki are less canon, since they should be completely mechanical. However, I think he said that just the organic parts are more canon, so I guess the most canon versions of the Toa would look exactly like the sets, but with the Mirimax muscles and organs on top. It’s really a case-by-case thing.
Even among the individual mediums, there’re inconsistencies- for instance, Makuta should look the same in Legends of Metru Nui & Mask of Light, sans wings. But, because of the description in Time Trap, we know that parts of this appearance should look as if they came from Krekka, Nidhiki, and Nivawk. So, basically, in this case, '03 Makuta gets retconned out of canon, with a wingless Ultimate Dume taking his place.