[vetinari]

If it is an ordeal, maybe you are doing something wrong?

Maybe your app sole entry point should not be a systray icon, especially, since users might not have systray at all (intentionally).

You will have similar issue with Android, and how it handles (persistent) notifications, background tasks and activities in foreground.

[lupusreal]

If it works everywhere except Gnome, requiring a custom solution on Gnome alone, it's definitely Gnome's fault. Gnome people have this weird ego thing where they expect the world to conform to them, even developers who are only including Linux support as a courteous afterthought to users. Anything Gnome does in a unique way adds friction for these developers, to the detriment of all Linux users.