hello trulso,
you may try using the Yocto-built rootfs image by untarring it in place of the sample rootfs.
however, you’ll need to ensure that the image is compatible with the NVIDIA-provided kernel and other components.
please see-also developer guide, Preparing for an Image-Based OTA Update, you should use l4t_generate_ota_package.sh by adding -f <rootfs_image> options to point-to the path of the rootfs image.