Since for flashing it is recommended to use a host system rather than a virtualized one (docker / vm) I did boot the PC with a Ubuntu 18.04 server usb stick and then mounted some free space from hdd for the use with sdkmanager.
Then I download the sdkmanager 2.1.0 and ran this command after connecting the Jetson via micro USB to host and setting it into recovery mode:
sdkmanager --cli --action install --login-type devzone --product Jetson --target-os Linux --version 4.6.3 --show-all-versions --target JETSON_AGX_XAVIER_TARGETS --select 'Jetson OS' --deselect 'Jetson SDK Components' --flash all --download-folder /mnt/test/tmp/sdkmanager --target-image-folder /mnt/test/tmp/nvidia/nvidia_sdk --license accept
After successful flashing and rebooting , the boot halts at the NVIDIA logo.
I also tried 4.6.5. here it boots further but then complaints about not finding PART-UUID=“” and then goes into reboot.
On this Jetson Linux RT 35.5.0 runs without problem.