I'm not an expert on Gnome Shell's behavior, since I don't use it. I'm
just going by what their developers wrote.

Auto-whitelisting the way you describe would be equivalent to having the
old-style notification area, plus a notification when an application
first launches, plus notification area items disappearing weeks after
the application was installed. I'm fairly sure that there would be no
understandable way of wording the notification that people would
understand. (If explained in enough detail, it would be too long to
bother reading. And suggesting that the user report a bug would be the
software equivalent of breaking the fourth wall.) And a notification
area item disappearing weeks later would seem capricious.

I just checked with the Unity 2D maintainer and he verified that the
whitelist works there.

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https://bugs.launchpad.net/bugs/773979

Title:
  legacy applications (using system tray) do not work in unity without a
  porting effort

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