I'm not arguing it. I'm arguing that if the definition of science fiction is the desire to explain things, Dune's status as science fiction would be iffy. At the end of the day, all fantastical elements in even the hardest science fiction boil down to hand-waving - the quality I'm talking about is how "buried" you want the hand-waving to be. Herbert was not very concerned with the plausibility of some elements of his universe, but he lavished quite a bit of work on the plausibility of others.
That's exactly my point. If faith is actually what makes a hexagrammatic ward work, then I don't see how you can call a hexagrammatic ward technology. If you can't build a machine that does what a psyker does, I don't see how you can call what a psyker does natural (contrast navigating the Warp, which can't be done without a psyker, with Dune navigators, which can be replaced by machines). If a psyker's power comes not from his mind but an external dimension, I don't see how you can call what he does psionics (the traditional science fiction substitute for "magic").
That's true, of course. What I'm trying to point out is that one of the differences between science fiction and science fantasy is in the effort put into obfuscating the fact that it doesn't work. For instance, neither Star Wars hyperdrives nor Star Trek warp drives actually work. Both are based on bad science, or at best unverified speculation. But Star Trek expends a great deal more energy than does Star Wars in trying to make its FTL technology sound plausible and describe exactly how it works, at least in-universe. That is [one of] the thing[s] that makes Star Trek science fiction while Star Wars is science fantasy.
To put it another way, Star Trek cares a great deal about how its warp drives work, as evidenced by the reams of paper spent "explaining" it. Star Wars cares only a little about how its hyperdrives work - there's an explanation, yes, but it's nowhere near as lavish as Star Trek's. Similarly, the fact that 40K explains the psychic mutation as the work of a single gene indicates to me that 40K doesn't actually care very much about how the mutation works, which to me is more indicative of a science fantasy attitude than a science fiction one.