Yubikeys are very useful. I was pointed to them by a colleague and was a bit skeptical in the beginning but since then I am more than happy to use them, absolutely flawless execution. The only thing that I am a bit concerned about is that it isn't the key that I place on the device that governs all this so you can't be 100% sure that there isn't some kind of supply chain trick that would allow the manufacturer or one or more of their employees to create duplicate keys.

With Linux I think you do have the option of encrypting with your own cert using the PCKS#11 module on the Yubikey.