I dunno if it's nessisarily subverting the Foreign messiah trope either particularly.
In parable there's a lot of overlap with the white messionic saviour trope just the indigenous peoples are obscured by sci-fi. The Fremen are depicted sort of as braves of the "noble savage" variety having an innate connection to the land in the form of their connections to sandworms, walking without rhythm etc and are visually othered blue by spice. Paul learns things about himself by their adoption and ultimately rises up through their ranks to lead them, takes a concubine in their ranks who represents his "love" but ultimately marries and legitimizes his connection to an offworld Princess. The Muslim/Islamic coding doesn't particularly help matters. The whole Sandworm thing is coded to bring to mind oil drilling. Uplifting the Fremen society is also not without consequence - doing so is destined to perpetuate a massive out of control religiously motivated slaughter across the universe... Which is not so great. Smacks a little of replacement narratives which puts emancipation always at someone's expense of being just replaced on a heirachy. Even the names Atraidies is Greek coded and Harkonnen is ripped from Finnish making the houses kind of White coded, particularly since the whole "Western Civilization" thing is often coded as the legacy of the Greeks and Romans (its part of why important government buildings basically are built to resemble faux Greek temples).
Paul also gets his powers basically from a Eugenics based breeding program which more or less legitimizes that process.
So while many look at Dune as a subversion of colonial tropes the framework that paints Paul as a devisive figure also sort of hinges on this idea of him being a good spirited race traitor who manages to become more Fremen than the Fremen whose fall from grace inevitably sparks the downfall and replacement of the (Western coded) civilization he comes from killing billions...
I recognize generally the instinct is to go with the kindest spirited read about these things which I can't slam anyone for. I don't think good faith readings aren't nessisarily a moral failure, it's human to want to extend the benefit of the doubt, it's just critique is evolving to see things more pluristically. People like what they like and this particular author isn't exactly reaping any benefits of influence, he died almost 40 years ago. People are gunna reintegrate his work to try and adapt it to modern attitudes just like they do with things like Tarzan, Lovecraft and Dances with Wolves. There is however a kernel of supremacy in the work, unwittingly placed or not (I haven't looked into the personal deets of the author's beliefs and maybe it's better that way) that is a product of the compounding and normalization of other like works that we are growing up to see weren't particularly good for everyone.
Maybe however my particularly harsh read is an extrapolation of my own background. I am a West Coast Canadian. We are encouraging ourselves as a society to have a really hard think about indigenous affairs and attitudes. Like its pretty normal where I am for all events, meetings and performances to be preceeded by a Land Acknowledgement and a lot of my friends in acedemia and the arts world are actively trying to fully subvert, credit or recognize and append this stuff so we can start dismantling the structures we're all unwittingly complicit in. I have buddies from the States who are pretty leftist who are just entirely mystified by the depth and breadth of the process. Yet I am no angel. I love the Anno series of video games which very uncritically depicts a very sanitized version European expansion and capitalist Empire. I watch and enjoy anime that routinely has aspects which are often ridiculously sexist in treating women more like beloved pets than people. I think Miyazaki was right about anime while still enjoying the fruits of that industry. So I am not gunna say "We should spurn Dune once and for all!" but like... I also think we can learn from it and not let it entirely off the hook.