I figured out a workaround for this.
The popup is being created in the RHIDetectAndWarnOfBadDrivers function in DynamicRHI.cpp
It’s actually looking at a console variable before deciding whether or not to create the popup.
If you add the following line into the [Startup] section of Program Files\Epic Games\UE_5.1\Engine\Config\ConsoleVariables.ini the popup should disappear:
r.WarnOfBadDrivers=0