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GNOME and AppIndicator/system tray
(startrek.website)
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Community icon by Alpár-Etele Méder, licensed under CC BY 3.0
Damn, this thread you've linked... I can't believe they didn't even want to consider giving the user an option to choose the behavior for themselves.
It seems to be characteristic of the Gnome project's philosophy to do things in what they consider the best way rather than the way a new user might expect. It's an admirable commitment to deliberate design rather than copying, but it may also make it unappealing to some users. Personally I don't enjoy using Gnome, but I know people who love it. Thankfully in the Linux world we have options.
I don't know if I'd call that "admirable". It's not the first time I see Gnome team basically telling the users "STFU, we know better".