I haven't read but Dune and Dune Messiah, so I'm definitely not an authority, but it seems to me that FH was interested in how the perennial things in mankind refracted against the new industrial/managerial world he lived in.
To look at how that worked, he created the post-Butlerian Jihad setting where mankind had integrated the rational and computational functions of an industrialised universe into itself instead of externalizing it. He concludes that those functions look indistinguishable from mysticism, per the Arthur C. Clarke quote. But I think what makes Dune unique is that by taking the implications of that conclusion seriously, he can reverse things to look at technique as spirit and treat race and heredity as technology. I don't think FH was thinking about religion or power or revolution directly, in either a cynical or positive way. This kind of stuff is just incidental to his noodling out whether personal effort outweighs inheritance as a technique for being in the world.
So I think the story's main point is the exploration of forms of marriage as technologies that allow or require mankind to survive. FH's thesis seems to be that there is a paradox in the question of being the world in the first place, where the self is a product of the world and creates it.
Then he wrote a bunch of other books I haven't read, so your mileage may vary with this idea. You got me excited with that italicised "thesis"! What do you think?