edit: I think it's solved, tested on 5D3: https://bitbucket.org/hudson/magic-lantern/commits/92536576a20d
Tested this solution on 500D, using srm-memory branch to build, works Ok.
I need to disable "Extra hacks" to get the AF working. When disabling the hacks, the AF works fine with SRM enabled.
I have done the "Don't click me" test with this changes, as you suggested, and I am able to take shots, record video and AF during the test.
But I don't know exactly how this test works and how it should be used, sorry

In first place, I do not know if the test ends after a successfull run, or if it runs continously until I shut down the camera, as I did
Disabling the "Extra hacks" is the key, also, for the Nightly build I tested earlier. Now I've tested it again, disabling the Extra hacks, and AF works (no SRM, of course).
When I tested the srm-memory branch yesterday, I disabled the hacks also, because some days ago, testing mlv-rec, I got errors when starting video recording, and Greg suggested me to disable them.
But today, whith the new Nightly build, I saw mlv-rec worked without disabling the hacks, so I left them enabled ... but that's the reason for AF not working.