regarding her Son leaving her behind the chemical to become himself I have to disagree because of two reasons:
1.) The Doc asked "do you know where you want to go?"
2.) The Doc also said the Son thought she wouldn't come back.
Because of that, my theory is the following:
Similar to "Interstellar" its not really a story about reality or consciousness but in the very basis a story about the love of a parent or the bound between a parent and a child. Therefore and because of how the animated world works she decided to live his life again (because she was there for most of it anyway) and at the end the audience is left with the decision wether or not their bound is strong enough so they end up together in the same subconscious place or if its just a fantasy of her.
I also wanna state that a reviewer on rotten tomatoes put it best "The Congress rises on the strength of Robin Wright's powerful performance, with enough ambitious storytelling and technical thrills to overcome its somewhat messy structure."
The structure is sort of messed up (maybe by choice of Folmann or maybe by the editor - who knows), but for me Robin Wrights performance and also the basic Idea behind the movie (both the story of love and the bond, as well as the idea of a possible drugged up future - which also has a metaphysical element to it: just living in your own head and creating your reality) makes up for that. which leaves us with a disturbing and sometimes artisanal bad, yet powerful and beautiful movie.
It seems to be more of a pitch, then a fully completed work