Trying to summarize your treatise, please correct if mistaken..
You're saying that Dune doesn't subvert the foreign Messiah due to the fact that Paul isn't shown to be wrong. As discussed above, for plot reasons and due to prescience. He represents a different face of Western colonial expansion and since a hierarchical undercurrent is always present, the subversion doesn't really happen.
Ugh, I agree. At least for his arc, it is shown to be a heavy burden but a necessary evil. It does propagate the idea "sometimes you just need to hand all power to one man who knows more than you". My bad.. I realize I may have been confusing the book and Villeneuve's portrayal of Paul (hope you do get to see it one day!).
For my education (as I am curious to hear you're thoughts [if you'll humor me but no pressure]), I will try to push the "benefit of doubt" narrative and still try to justify Herbert a bit in regards to the pluralistic viewpoints you've laid out.
I get what you mean by seeing the broader context. The Fremen are shown to have a fluid government, more democratic than the Empire. They have more connection to the land, understand their shared history, value of life, value of resources and balance. I'm imagining a rosy native tribe close to nature, drugs and shit. Paul goes there, learns how they live, somewhat adopts their values and is free from the matrix.
If Paul is shown as narratively perfect, then the 'indigenous' views he carries are also weighed higher than the Imperial mindset. Yes nothing may have changed since the Fremen slotted into a hierarchical structure and paid for it, I think still Herbert acknowledged that indigenous views were 'better'. A 'civilized' white man didn't teach them a better way of living, instead he was corrupted to their way of thinking and worked with them to defeat the Empire.
As to wielding power and somewhat adopting a hierarchical mindset, I naively believe that intentions matter. In Paul's example, he had the bestest of intentions. If there was no war, I think he would happily abdicate power, fulfill the dreams of the Fremen by giving them a healthy ecosystem and go live with his love (I would sidebar argue he actually loved Chaini and kept the princess as his concubine). I know power corrupts but what could he do other than fight for what he believed in.. I know it's all on trust and faith and lovey dovey stuff.
In your case, you acknowledge structures you're complicit in and with what power you have, you are trying to nobly change for better. Yes wielding power can be done "humanely" by asking for permissions and consulting everyone before making decisions etc.. but in times of urgency/high stakes, autocracy with a philosopher king/Jedi Master/Omniscient Paul is generally preferred. People who may try to fight you/Paul, probably do not want to pay the price of emancipation/equality. How else are we supposed to enact change other than using our power over others?