No, you can not assume that movies aimed at a mass audience are documentaries. Theatrical movies are meant to entertain a high number of people in a set amount of time. So, it's no surprise that they are inaccurate. Made-up drama and character mashups are going to beat facts. If people want factual accuracy then you should stick to documentaries and history books. Theatrical movies will always be inaccurate and that's ok. I watch movies to be entertained.
Art is in the eye of the beholder. To us, a work may have meaning and evoke emotions that the creator was totally ignorant existed.
However. I suspect the deep political allegory this author finds in Amadeus may be unique to their perception. I wonder if they find similar complexity in other things: does the wind contain voices for them? Do the voices tell them to "do things"?