I tested 5.20 from Shuduo's PPA and for me it reproduces the issue just
the same as -proposed. To be sure, I then went back down to release
versions in all the other packages (so that the only change wrt.
released is again just Unity being 5.20, just now from the PPA), and the
issue remained. Downgrade Unity to 5.18 and it again goes away.

But this looks like a speed issue, so Unity may not be directly at
fault: any apps started once the desktop is fully loaded open as truly
maximized, so a workaround is setting autostarted apps to start after a
delay. Perhaps Unity going from 5.18 to 5.20 here causes just enough
delay for those apps to start before whatever the component is that
should fuse the menus with appindicator. The autostarting facility
should wait for that component, or the component should be also able to
fuse menus for existing windows once it gets up and running.

Incidentally, any appindicator-related packages' versions also don't
seem to matter for this once Unity is 5.20. I think I'll try upgrading
just those to their -proposed versions next (so that Unity remains at
5.18) just to cover all angles.

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https://bugs.launchpad.net/bugs/1195730

Title:
  Maximized windows opened during login not actually maximized (when
  using 5.20 from -proposed)

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