Yes, we did have to pair the Yubikey and AD accounts with an admin account. It was going to be a lot of work, but (at that time) we were only going to deploy about 400 if we used that as our final solution, so we just planned to have multiple admins with the capability and deploy in waves.
Those directions are significantly different than what we did. Apple has been 'enhancing' native smartcard support since they are (allegedly) making more use of it, and those instructions appear to be using that native capability.
When I had to set it up, I had to compile a third-party version of smartcard services and then use the Yubikey apps (like the Yubikey PIV Manager) and the Apple keychain to get everything working. It wasn't fun to setup, but worked reasonably reliably once the parts were in place.