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
The user experience is nicer as a native app, if done right. With a PWA, you have to deal with anything crappy that the browser inflicts on you, and the developer largely can’t do anything about it. For example, Chrome sometimes just crashes or freezes entirely on me, which means Voyager can too.
See elsewhere in this thread for examples of little things that stem solely from being a PWA .
Don’t get me wrong, I think Voyager is great for a PWA and it probably gets a lot of value out of being a PWA making it easier for people to contribute. But it’s just not as good as native for me.