If I quit iTerm2 I always get the "Quit iTerm2? All sessions will be closed." message - independent of the settings in preferences. I don´t tick the three options under "General/Closing" - all regarding the closing mechanism. Normally the message doesn't have to appear, does it?
It´s annoying that I cannot reboot my system without explicitly quitting iTerm2. If I don´t close is by myself the system will hang/block the shutdown.
Well, after upgrading to Sierra and installing latest version of iTerm2 I've got the hint from iTerm2 self: In "Profiles" there is an option into default profile (Tab "session") named "Closing" which was always "on" - after setting to "Do not prompt before closing" the behavior of iTerm2 is like expected.
Under "Preferences" -> "General" -> "Closing" was a "Confirm 'Quit iTerm2' command" checkbox which worked for me. The "Profiles" -> "Session" -> "Closing" -> "Do not prompt before closing" option did not help with the shutdown case.
