Any story has an implicit assumption about the kinds and levels of absurdity you can expect. People get weirded out when you violate those expectations. Marvel, by virtue of their source material if nothing else, has set a much higher baseline of goofiness for their movies than most others. Whereas we all sort of know Dune was meant to be Serious Scifi. And I guess people who decide they like the Lynch adaptation have re-calibrated their expectations, and found the movie internally consistent on some level. It's all about audience expectations (and sometimes Hollywood ignorance/laziness, I guess).