I don't run FreeBSD, so perhaps a FreeBSD user with a Yubikey will chime in, but as I understand it FreeBSD has Firefox and OpenSSH, and both these programs can use the FIDO feature (which is the focus of the article) on a USB Yubikey to authenticate you successfully to a remote system so it ought to work out of the box on up-to-date software.
The other features like using it to store PGP keys are a bit more fiddly to set going and you may need to read instructions specific to FreeBSD for those.
Only the weird Yubico-specific OTP thing is a keyboard. The FIDO features are HID (Human Interface Device, the USB protocol for keyboards, mice, etc.) but they are not keyboards, when asked what sort of thing they are in HID they say they are 0xF1D0 ie FIDO devices, which means software looking for them can find them in order to speak the FIDO sub-protocol. I presume the PGP key stuff similarly uses its own standard protocol.
The other features like using it to store PGP keys are a bit more fiddly to set going and you may need to read instructions specific to FreeBSD for those.