I thought I'd report this experience here. I don't believe it rises to the level of filing an Issue on github, but it is interesting.
An employer of mine uses DUO to authenticate. I have used their Duo MFA on my Graphene devices for years. However, they instituted a new policy where tampered devices are now blocked by Duo. I received an email that Duo reported my device to my employer as "jailbroken or tampered."
It turns out Duo simply checks Play Store to see if your device is Play Protect Certified. You can check this yourself under Play Store (only if you're logged in) - Settings - About - Play Protect certification. It will say Device is not certified. If you click Fix device issue it will perform a lookup for a bit - likely just checking Google servers to see if your device is listed? - then fail.
Note, this is not the same as Play Protect, which is an agent which scans user-installed apps for malware. Play Protect Certified apparently just reports whether you are running a device which Google, Inc. has licensed. That's it, as far as I can tell.
Ironically, even an old, very insecure, out-of-date Android device will likely still pass this check. Read this GOS discussion for more info.
So Duo does not check your OS, or your bootloader, or whether the device is actually tampered or rooted. It simply pings Google Play Store app and asks if you're running a device which Google has a licensing agreement with. That seems like a very lazy check, but I guess it is effective.
Note, Duo used to work fine on Graphene (with Play Store, with Play Store not logged in, or even without Play Store installed, albiet push notifications don't work in that case). So this is probably due to a new workplace policy. Duo must have reported my device as tampered for years, but my workplace did not have a filter in place to block access.
Either that, or Duo recently updated to include this check. (I doubt Duo would document this, but someone can check.)
Even now, I can still install and operate Duo. I even get a rotating 2FA code! But when I enter that 2FA code on any device, Duo gives me an error message that my device is tampered and the entry is not accepted.
Also, Duo push notifications are still pushed to my "tampered" device! Which seems wild to me. But again, they are not accepted.
My cybersecurity team said that it may be possible to sideload the Play Protect certificate for Google Pixels. However, I have my doubts.
I did see that Google offers a way to register your device so it is Play Protect certified. However, I cannot run adb root - it says root access is blocked in production builds. Per this discussion forum post, it sounds like that won't help anyway.
Finally, I guess one option is to email Duo to request they change their check to allow GrapheneOS to pass, and there are suggestions on how to do that here. But Duo doesn't seem like the most user-friendly company. Corporations are their main customer, not end users.
Any thoughts are appreciated, but unfortunately I consider this an intractable issue due to Duo's (lazy?) check of Play Protect Certified status.