Hello
The difference in the Manufacturing tool with rootfs and without rootfs, I explained you in your other community question.
Manufacturing tool for iMX
Manufacturing tool doesn't need to be installed, is an executable file. You only need to run the script, but take note that you need to have the image in the correct folder. Otherwise, the script won't work.
To program the emmc, you only need to run the correct script that allows you to program the emmc.
Best Regards,
Diego.