I just got to thinking about this. Perhaps, TAS has two layers of canonicity. One layer is with the live-action sequences, why may be more "real" - where he recounts flashbacks of things that have happened. Then there are the animated series, which are "less" real - and modified for that sake of entertaining children. Now, when I say "canonicity", I mean in the context of TAS alone - not in the context of any relation to the films' canon.
As such, perhaps, we could imagine that the events of TAS did occur - but not necessarily in every little detail as they were shown.
That said, in the live action sequences, I do wonder who Doc was talking to (in-universe, that is). I figured that it probably could fit in with the Ride-verse, where Doc and his assistant are relating stories to and teaching budding young scientists. Perhaps, there's a specific wing in the IFT for young children who want to become scientists.