I do agree that the construct of a command structure was formalized in voyager. I do think the very introduction you quoted still completely imploded the borg as a concept. Data even is directly pointing it out. The queen is just hand-waving it away without actually answering.
I think the ambiguity in explanation was designed to let the audience to just "fill in the blanks" however they wanted. I think the writers just said "who cares, it's a movie, TNG is over, we can fuck the TNG universe".