One thought on this: If you were to take the content of all of those partitions (without signature) and replace the content in the flash software (those partitions have binary files in place, and if flash parameters are set, then those binary files are signed and flashed), then your version of that partition would get flashed. Assuming the content is the same, then other than perhaps the signature, this would be the equivalent of leaving those partitions alone.
I suggest you create a log during flash on command line as a reference to see what gets flashed where. Example: sudo ./flash.sh jetson-nano-emmc mmcblk0p1 2>&1 | tee log_flash.txt