The flash program itself only runs from Linux. The file system can be re-used, so that step can be done once and not repeated (saves a lot of time).
Some details you may be interested in…a Jetson TK1 arrives with R19.2 (I don’t think this has changed, but perhaps it has since I got my JTK1’s a couple of years back), which defaults to using fastboot. The nature of fastboot is that if you want to change anything you have to flash to change it.
R21.x and up use u-boot. If you’ve flashed your Jetson to a recent version, you’re in luck since pointing at a different root partition is as easy as a short edit of “/boot/extlinux/extlinux.conf”. You could easily install a custom rootfs on SD card and edit extlinux.conf to point at the SD card without using flash software.
Jetson, upon boot, points at a boot loader; boot loader points at a rootfs. Flash with “mmcblk0p1” and u-boot places boot loader on eMMC, but because of extlinux.conf rootfs can still go anywhere. Flash with “mmcblk1p1” puts the boot loader on SD card, and the boot loader binary itself must be on the SD card if boot is to continue. Simply putting a rootfs on SD while u-boot is on eMMC is easy…I’m not sure what you’d have to do to clone the boot loader binary onto SD card if “mmcblk1p1” is used.
A very subtle and big complication if you do not use Linux for file copy (notice I did not say binary clone) is that Windows cannot format an SD card to ext4. Windows also does not understand Linux file permissions and several file types. Directly copying or creating file content from a Windows machine will end badly, but you may not notice until strange things happen. Clone operations which do a bit-for-bit file system copy (and thus do not need to understand partition types and file types) will work from Windows. Unfortunately, Windows may not come with software required to do bit-for-bit creation of partitions on an SD card (the underlying file system itself would have to be a bit-for-bit clone).
A key to knowing what will work best for you depends upon whether the images your tech applies need any kind of editing or not.