I don't know about this "root key" setup you describe, but you can certainly program sets of yubikeys with the same OTP secrets at setup time, resulting in clon

I don't know about this "root key" setup you describe, but you can certainly program sets of yubikeys with the same OTP secrets at setup time, resulting in cloned/backup keys. The OTP secrets can also be stored (presumably offline) to create new copies of the key in case of recovery.