I agree with you. It is a simplification and I generally like the Zone System (Adams/Archer, not the variations by other people). But I think many people who read about the Zone System misinterpret it as a way of directly controlling all the print values with negative exposure and processing. Very broadly, perhaps. But not really. If that is the way someone wants to work, he really needs a better understanding of the transitions from subject to print, the variables, controls and limitations.
I also agree with your last statement, which was more or less the point I was getting at. The more rigourously you "extend" the Zone System by applying exposure theory and tone reproduction theory, the less use you have for the simplification model.