Hi. As I am not really "fluent" in Raspi Pis or CM4s or such, my process is as follows.
Installing your software: I had your software copied to a USB stick, inserted that into the Interceptor board (with the CM4 attached to it, of course). Attached a monitor to it via HDMI. Then connected power, and waited for that little menu of yours to appear. I chose "install", it installed well and works. I am NOT using a SD card, my CM4 has eMMc storage(or whatever the storage on the module is called)
In order to back up the whole system, i want to create an image of the software on the CM4. I thought the only way to achieve that is to take the CM4 out of the Interceptor board and plug it into an IO Board. The IO Board has a switch that allows me to start the CM4, showing the emmc storage as a regular drive in Windows 11. So then I can use Win32DiskImager to make an image of the software on the CM4 (I just create an image of that drive that is the emmc storage of the CM4) and save that away.
With your software on the CM4, the CM4 does not boot into that specific mode.
So now I do not know how to create an image of the software on the CM4. I am not aware of how this would work with the CM4 in the INterceptor board.