Yes, you can't touch any keys etc .. or the shot is taken immediately.
Yesterday, I set the timer at 30 seconds and had plenty of time to minimize the terminal and set up other windows for the shot. Once the timer is going, the script (or scrot) releases focus/control.
The color of the rectangle is apparently a scrot internal - I cahnged my desktop colors and the rectangle is changed to be visible - some color matching code within scrot.