Below is a quick test combining full resolution silent pictures with another useful Magic Lantern function: Focus stack. It lets the user set start and end point of the stack and number of autofocus motor steps between frames.
94 frames on EOS 6D with smallest step the Canon 100mm Macro 2.8 USM (non-L) can take and starting almost at closest focus (1:1). 1 second exposure at full aperture. Available light (lamp in the ceiling of my livingroom). Stacked with Zerene Pmax. No further processing.

I doubt flash will work with this method since normal shooting from live view does not trigger the flash. I am going to try a setup for my DIY "stackshot" with separate triggers to the flash and to the camera (with suitably long exposure time and darkness in the room). Unfortunately that requires changes to the remote cable since the silent picture readout is triggered by shutter half-press. Something to do in the weekend

/Bo