hello sebastien.schertenleib,
please refer to EKB Header, JP-6 reads FV from the input EKS image at offset 16.
you may dig into gen_ekb.py from nvidia-jetson-optee-source.tbz2 for details.
yes, you may adding --uefi-keys ~/Keys/uefi_keys.conf to the command-line for creating the OTA update payload.