I am just posting this for, hopefully, the benefit of others. I have been searching for a good motion detection solution for wildlife photography. I have a Canon T6i, but alas, no Magic Lantern. I saw I could buy older camera bodies online for reasonable prices. I bought a Canon T3(1100D) but found that the motion detection via Frame Differential didn't work. I sold that body and picked up a Canon T1i (500D) the motion detection and the frame differential worked but the auto-focus did not. I sold that and bought a Canon T3i (600D) and it is works great. Motion Detection, frame differential and auto-focus.
The moral of the story, if you need these features, I would recommend the Canon T3i. I know everyone uses Magic Lantern for different purposes, but I couldn't find any good information on what works for my particular need.
One additional note. The Canon t3i has the screen that flips out. For motion detection, you can set it up and then flip the screen around so that the screen is facing the inside of the camera, which will switch off the screen but continue to monitor and photograph. You get much better battery life from this setup.
I seriously doubt AF in motion detection is working properly because it is a known issue on various cameras (both Digic 4 and 5). See issue #2923. (https://bitbucket.org/hudson/magic-lantern/issues/2923/feature-use-autofocus-breaks)