40K is a scifi setting I rather like, in part because these issues don't really apply to it. It's an extremely magical setting where magic tends to permeate almost everything. Even the "nonmagical" tech is explicitly more akin to fantasy magic than most scifi, since most people don't understand it at all in-universe. And of course it's just really silly, which helps. A lot of scifi takes itself much too seriously.
That's really the core of my issue--most scifi tries to justify itself as somewhat realistic, with most real science being accurate and applicable, but with random exceptions as needed, which don't have the large scale ramifications I'd expect from them. It's "realistic, but with a spot of magic here and there", which is much harder for me to accept than a straightforward "yeah the whole world is magic, it's totally different, the planet's prolly not even a sphere and is likely the literal center of existence." In a fantasy setting, chemistry probably doesn't exist; fire is more likely to be a metaphysical concept directly drawing power from some entity or law of nature, rather than any kind of chemical reaction. In a scifi setting... it's generally going to work just as it does in my world unless explicitly stated otherwise, which means I'm supposed to understand it, and that causes issues.
As for communications stuff, yeah, you can usually write around it. The problem isn't so much that it can't be handled, it's that it's usually not handled. And scifi settings will have communications technology as a given, while fantasy settings have to deliberately choose to make that mistake. And they'll prolly still have an easier time with it, because they can just stipulate some extra random rules for the magic comm rocks to justify whatever the story needs.