FYI, a recovery mode Jetson is not a mass storage device. In order to access that disk with dd the system must be fully booted. At that point you could not guarantee that the filesystem wouldn’t change while using it, although you could perhaps set it to read-only before the clone. Or you could just use the raw clone and get the exact same dd copy from the Jetson. It is the restore part which may not work the way you want it to work, especially since it isn’t a mass storage device.
A lot of people also fail to consider that a full flash is also flashing other non-rootfs content, and part of that content is equivalent to a PC getting a CMOS BIOS flash (but a Jetson does not have a BIOS, so this is spread out in software in other ways).
Incidentally, if you use the correct tools for clone, then you get a loopback mountable raw image which can be examined, edited, and used again for flash. There is also a “sparse” clone which is useful only for flash. I tend to delete sparse clones and keep only the raw clone. Beware though that this takes a long time and it is an enormous file. If your rootfs is 64 BG, then so too is the raw clone; if the system is half full, then the sparse clone is another 1/2 of 64 GB, or 32 GB on top of the raw clone. Sparse clones were invented for faster flash since less data is needed.
You might be better off actually describing the problems in detail if you want a better answer. Cloning is part of the flash software on command line and is a perfect bit-for-bit exact rootfs copy just like dd is, but it uses a recovery mode Jetson.