Comment by amlib

But then you run into the problem of apps assuming the tray icon exists or is visible, but isn't, leading to problems such as the program just disappearing when you close it's window with no way to reopen it (some do reopen when you try re-executing it, others do nothing or just spawn a whole new instance...) or even having no access to some function that is exclusive to the tray icon menu.

All these issues can happen in any platform, Linux is just the more annoying/unpredictable one, with GNOME taking the cake for being so obtuse. There is either a carelessness from the developer or the ad-hoc nature of those "tray icon" systems is to blame.