Are you asking for the mechanical shutter to be open at all times and use the cap to cover the camera or scope when taking dark and bias? Of course mechanical shutter needs to be open for lights and flats.
I don't know if you are aware of this. Many capture software allows you to control the mechanical shutter. You can tell the capture software to keep the mechanical shutter always closed for dark and bias. I am not sure if there are capture software to always keep mechanical shutter open at all times. I use Nebulosity and SGP for capturing images and I do not see an option to keep mechanical shutter open at all times.
I always keep mechanical shutter closed when taking dark and bias via capture software. In other words, mechanical shutter never opens for darks or bias. But for lights and flats, mechanical shutters always opens and closes.
Mechanical shutter is useful for remote control for taking darks and bias when you are not near the camera/scope.
Sony CCD in QSI 660wsg camera is interline meaning mechanical shutter is not required but QSI put it there anyway for not only for remote control for taking darks and bias but also good protection against foreign elements like dust hitting the CCD.