(See the best response by Spevacus.)
How do I set Byond to shut down fully when I close it without having to go to my system tray to shut it down?
Best response
On the pager, clicking on the options button (Cog wheel on the right side, below the red X) and then clicking "Exit" will fully close BYOND's Pager.
That's obnoxious, but thanks
Ctrl + Q will also cause the pager to exit.