One of @FauxLiving@lemmy.world’s comments linked to a bug report about it. Turns out the real reason is that Krita uses a plugin architecture that allows additional file types to be supported, so it can’t actually know the complete list of MIME types to put in the .desktop file at application install time.

Krita makes it possible for plugins to extend Krita with additional file format support. Those plugins come with a desktop file that tell the desktop that krita can load those file types. Of course Krita’s main desktop file cannot have the full list of supported file types, because that’s implemented by plugins. Most of those plugins are shipped with Krita, but that is not necessary. People can create extra import/export plugins that still need desktop files so your desktop can know that Krita can load this file format.

I’m not completely convinced that’s a good reason (compared to, say, having each plugin installation modify a single krita.desktop file or something), but I think it manages to upgrade it from “indefensible.”