There is one way you can backup the whole contents in eMMC to one IMG file. After the backup, you can apply the IMG file to other devices.
Please follow these steps:
Make the eMMC work as a single storage device on a PC. To do that, please refer to the section 3.4 Writing images to the eMMC in the following online document: http://mueblesavantdeco.com/docs/os-manuals/cortex-a53-raspberry-pi/debian/
Use win32diskimager to read the IMG file from the eMMC on your CM3 or CM4: http://sourceforge.net/projects/win32diskimager/
Use the new IMG file to flash to other devices. Please check the 3.4 Writing images to the eMMC chapter in the online document:
http://mueblesavantdeco.com/docs/os-manuals/cortex-a53-raspberry-pi/debian/