Hi hogank,
My steps is following Developer Guide (the same with your first comment).
I don’t change any file, using default image download from SDKM.
List test steps for you reference:
1. Check the flash drvier's device name:
$ sudo lsblk -p -d | grep sd
2. Create a new GPT:
$ sudo parted /dev/<sdx> mklabel gpt
3. Add the APP partition:
$ sudo parted /dev/<sdx> mkpart APP 0GB 16GB
4. Format APP as ext4 partiton:
$ sudo mkfs.ext4 /dev/<sdx>1
$ sudo mount /dev/<sdx>1 /mnt
5. Generate the rootfs without flashing the device:
$ sudo BOOTDEV=sda1 ./flash.sh --no-flash jetson-xavier sda1
$ sudo mkdir tmp_system
$ sudo mount bootloader/system.img.raw ./tmp_system
$ sudo rsync -axHAWX --numeric-ids --info=progress2 --exclude=/proc ./tmp_system/ /mnt
6. Umount flash driver:
$ sudo umount /mnt
$ sudo umount ./tmp_system
7. Plug the flash drive into target device and power on.