Is there a way to shut down, restart or log off without seeing the popup?
There are a few methods to shutdown without confirmation (this will not remove the confirmation from the original method):


In Terminal: shutdown -h now, but this force quits all applications
Make an Applescript and save it as 'Application,' save it somewhere easily accessible, but not prone to accidental clicks: 


on run
  do shell script "shutdown -h now"
end run


The shortcut Control-⌥ Option-⌘ cmd-⏏ Eject
Clicking shutdown with ⌥ Alt / ⌥ Option held down (as you said)
If using Alfred, you can summon the Alfred window and start typing "Shut down" or "Restart" and then pressing Enter. No Power Pack needed, no force quits, no dialog and no countdown.


You could also try following this method by WZZZ, but I haven't checked if it works. It reduces the time to auto-quit apps, so do: 

defaults write org.x.X11 wm_auto_quit_timeout -int x