Any luck performing the DotTune procedure manually, as explained by the author (horshack) ?
For example, if you hold the camera still, focused on the chart, and you change the AFMA value to some extreme values (say +/- 100 or whatever the menu allows), do you still get focus confirmation? After some threshold, you should no longer get the confirmation.
Maybe the focus chart is "too sharp" and you still get AF "confirmation" even if the image is somewhat out of focus? Just a guess; back then, I've only tested on regular subjects (i.e. something with fine print or other sharp details, but not on a dedicated focus chart). I did not test on 6D, but other users reported success.
Otherwise, I'm out of ideas. You could try looking at previous posts for suggestions, but I guess you already did that.
I'd still like the logs, if possible. It won't cover the entire dot_tune process, but as long as it catches a few AFMA value changes, it's fine. Manual adjustments from both Canon and ML menus should be covered, too (just scroll through a few values, nothing fancy).