Created attachment 234340 [details]
screencast

If you are accessing an icon's menu from the "tray mode" (super+M), it will show up at the correct relative position but close the message tray (I suspect it shouldn't, until the menu is actually closed by clicking outside the message tray);

However, if you access it from the message tray while the Activities overview mode is active, the menu will be positioned below the bottom edge of the screen (?), making it scroll needlessly.

Attached screencast demonstrates the difference.