I am kind of lost in this discussion, but let me just ask one question.
Won't all of the proposed solutions, other than the one of just not expanding transclusions that can't be expanded to wikitext, break the original and primary purpose of ExpandTemplates: providing valid parsable wikitext, for understanding by humans and for pasting back into articles in order to bypass transclusion limits?
I feel that Parsoid should be using a separate API for whatever it's doing with the wikitext. I'm sure that would give you more flexibility with internal design as well.