Hopefully you don't mind the bump, but I'm interested in hearing whether it would be possible to fix this persisting problem with today's knowledge and experience. I just tried it with the most recent build, and it's still present.
Would you like me to post a video of me operating the camera, where I enable FPS override and adjust the related settings, all the while filming the camera's LCD screen and the button panel? This way, ML developers without 6D could see what the problem looks like exactly.