The immediate issue I have is with the FKMS driver. The Waveshare touchscreen requires me to disable the FKMS driver and use its own configuration, especially since I want to rotate 90 degrees. But if I disable the FKMS driver, RetroPie runs into the SDL/EGL error and will not load the GUI.
On the PI4, disabling the (f)kms overlay/driver will result in an unsupported configuration, with any GPU drivers disabled. You won't be able to use RetroPie with it.
Is there a different driver I should try loading, or do I need to submit a feature request and wait?
No, there isn't. Not sure why the Waveshare screen needs the standard Pi4 GPU drivers disabled - maybe because of rotation support ? In any case, using both screens will require X11/X.org running, at which point you may be able to rotate the display/screens using xrandr/arandr. It's not a supported configuration for RetroPie, but it may help you using both screens at the same tie.