With the help of @solene, I was able to quickly setup OTP logins through xscreensaver. I had already setup AEM and have my LUKS password for drive encryption. But since I use my laptop in public spaces and sometimes have to logout and walk away for a moment, I wanted to add OTP as the only login. I'm sure there will be some feedback on the security of this, so please do share any that arises.

First, download google-authenticator in dom0: sudo qubes-dom0-update google-authenticator

Walk through the setup instructions which will also generate your QR code for your auth app of choice:

Do you want me to update your “/home/jlwallen/.google_authenticator” file (y/n) y

Do you want to disallow multiple uses of the same authentication token? This restricts you to one login about every 30s, but it increases your chances to notice or even prevent man-in-the-middle attacks (y/n)

By default, tokens are good for 30 seconds, and to compensate for possible time-skew between the client and the server, we allow an extra token before and after the current time. If you experience problems with poor time synchronization, you can increase the window from its default size of 1:30min to about 4min. Do you want to do so (y/n)

If the computer that you are logging into isn’t hardened against brute-force login attempts, you can enable rate-limiting for the authentication module. By default, this limits attackers to no more than 3 login attempts every 30s. Do you want to enable rate-limiting (y/n)`

You can comment-out the auth include system-auth line if you don't want to enter your user password after entering the OTP, or keep the line uncommented and have both OTP and a separate user password. NOTE: Do not comment out account include system-auth

EDIT: oath-toolkit may be an alternative to Google authenticator. I will test soon. EDIT2: oath-toolkit is similarly used by AEM/Trenchboot.

OTP for xscreensaver [Guide]