I have the answer you seek.
Boot into recovery mode (Cmd+R while booting) and then open the Terminal.
cd /Volumes/Macintosh\ HD
//if your drive is named something different, replace accordingly
csrutil disable
//disables System Integrity Protection
mkdir AppleInternal
//activates testing and custom commands in Apple apps, including Simulator
csrutil enable
//re-enable System Integrity Protection
reboot
//back to regular environment
Now there's an "Internal" menu in the Simulator. In here, you can change loads of settings including the window's background color. It uses the regular OS X colour picker so you can even choose a hex code.