They probably just realised they'd created a much more complex fictional society, and that the behaviour would need to change to match it. The Rufus thing probably wasn't intended to be deconstructing tropes. They usually just lazily default onto a kind of romanticized feudal society, which would never actually exist anywhere but is nice to imagine. Most of the previous games in the series, and all RPGs since then, don't even bother doing this. It has clear political and economic structures that affect the world in understandable ways. The main thing FF7 did was just put 10 times as much thought into the details of the society it was depicting.
