It is a limitation of a PWA. A native app (wrapper) will likely be coming though, and a custom Capacitor plugin could theoretically interface with the native API to switch out icons. Theoretically. No promises though :)
Quoting this comment by the dev
Native as just a wrapper with some extra features I guess.
I see not wrong having both, I think the key of Lemmy’s adoption is how easy is to recommend Lemmy by just pointing to an instance with Voyager locally installed as m.lemmy.world.
Voyager should still be developed as PWA.