The previous idea of using a clone to flash from would work. @mdegans gave steps to add the right repositories to make adding these from a running system via apt-get. Then clone.
If you want to add these to the sample rootfs prior to flash, then apply_binaries.sh will not add the optional content for you. You could perhaps use QEMU to run apt commands on the sample rootfs as if it were a running Jetson. @mdegans happens to be good at this! :)
There is a script here you could examine, it is for adding an account before flashing so that the first boot content is already in place. You could study this or edit this (it is a script) to work with packages if you know what the packages are:
https://forums.developer.nvidia.com/t/jetson-nano-all-usb-ports-suddenly-stopped-working/75784/37
From @mdegans, very useful to study.
apply_binaries.sh will never add this content. That script is for content required to boot and run, and does not work with anything optional.