This has been a long-time issue (albeit caused by external projectors/monitors, not the nVidia driver itself). The easiest way would be forcing X to recognize 2 monitors at boot-time, assuming we always run in 'Clone' mode. You may extract relevant session in the xorg.conf generator here:
Use 'TwinView', set the desired resolution and add these lines into your /etc/X11/xorg.conf
Option "Twinview" "TRUE"
Option "TwinViewOrientation" "Clone"
Option "SecondMonitorHorizSync" "0"
Option "SecondMonitorVertRefresh" "0"
Option "MetaModes" "800x600 , 800x600"
Option "ConnectedMonitor" "CRT , CRT"
Modify those accordingly and restart X, it should work. The problem is you may experience undesired behaviors with a few applications that depend on resolution (e.g. games).
I have no clue why nvidia-settings doesn't allow forcing external monitor into a particular mode, given that the user has been warned.