Stepping from the issues of social strata IRL, back to the issue with social strata in the Duniverse, it would seem to me that all authors involved believe it to be inevitable for current (!) humans, although that may well be one of the themes as well.
Substantial spoiler for the prequels about to commence. Are you going to read them? If so, you’ve been warned.
Even the pre-Omnius (machine intelligence core) society, despite being based on the support of countless AI and complex machines had serious social inequities, with wealth (including merchant princes), caste (with planetary princes), and military structures. The last may or may not have been more ceremonial than effective, since we don’t hear much about it (other than it’s destruction), but the first two played into the fall of the Old Empire at the hands of the Titans.
The Titans themselves were part social re-structuralists and part wannabe cultists - in that they were following a popular philosopher who was pointing out the growing decadence of the Old empire. They usurped the AI network to rebuild the Old Empire and afterwards increasingly became entranced with their own power and glory, especially after they remade themselves as cymeks (brains in jars with mechanical bodies) to avoid death from old age.
So even the ‘greatest’ society of human history, which had nigh-unlimited slave labor (AI, although arguments could be made), still kept such elements.
One of the Titans let his personal AI gain too much independence due to laziness, and the system was upset, with Omnius (the machine overmind) now running everything, keeping the Titans around due to certain hardwired limitations, but as second class citizens, all the rest of humanity as slaves fundamentally. It is interesting to note, that even Omnius seems tainted by this tendency, as he refused to alllow any other independent AIs off Earth, where he has a single one as a companion. Although part of that could be argued as a result of his programming, rather than his very arrogant behavior.
Okay, so we have, to a degree, every society, human or machine, being quite pyramidal in nature. It is interesting to note, that of all the ‘active’ societies seen, there is one that seems quite interested in changing human nature itself, and has the least directly materialistic inner society - the Bene Gesserit. They differentiate between ‘humans’ and animals, and seek to create a better human. Their actions are certainly impure, their motivations may be less so, although far from certain. Still, with the society we see on Chapterhouse as well as elsewhere in the ‘core’ novels, they do tend to treat each other with empathy that borders on the titles they use: Sister and Mother.
They do not internally have a great deal of differentiation in wealth or external trappings, although those of higher rank certainly have a great deal of influence and soft power, with a great respect for wisdom, intelligence and learning, almost utterly divorced from the extreme social castes of the rest of the Empire, even though a number of Bene Gesserit are wives and/or concubines of some of the most influential individuals of the Empire.
Okay, enough of a book. Back to the OP, it is interesting to me that if you have slogged through the Sequels to the core books that the theories about collective uprisings and the dangers of controlling religious are utterly debunked: Because at the very end, individualism wins the day when the advanced Face Dancers have become the people they were ‘imitating’ and the Ultimate Messiah was born who will save everyone from themselves. 
Which is why I will recommend the House books (good), the Butlerian Jihad books (pretty okay), but not the sequels (very, very meh).