Ubuntu and KDE have standardized on the same indicator API, so the "the
standard way of doing things, and also the Ubuntu way" are one and the
same thing. The reason freedesktop.org hasn't adopted it is that Gnome
designers decided they didn't want third-party applications in their
panel at all, whether using the notification area or any other
mechanism.
<https://live.gnome.org/GnomeShell/Design/Guidelines/MessageTray/Compatibility>
If anything, it is Gnome that is in its own parallel world, not Ubuntu.

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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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