Can I user CAPI 2-factor authentication in MobaXterm?

Load your CAPI keys into PuTTY-CAC's Pageant (SSH signature agent). MobaXterm supports using Pageant for authentication (partly because its SSH client is indeed based on PuTTY). This also works with a few other clients, such as WinSCP or Bitvise Tunnelier.

As MobaXterm is compatible with Pageant, you can select the option "Use external Pageant" in SSH option, and use PIVageant as the agent. I developed it for my own purpose. It uses the PIV key storage to auth in a server. That would require at most some customization as the current configuration if for 9E pinless slot, and also it is focus on Yubico 5.