Up to now I have thought that when using CAF+TR the green square with small lines from each side meant that the camera had focused on that spot. It turns out that, on the E-M1ii and E-M1X at least, it means that the tracking system has locked onto that part of the image and it is the normal green dot, or beep if you have it turned on, that indicates focus has been achieved. Normally this will not make any difference but if you are using the focus limiter then the green tracking box may appear but if the subject is out of the focus limiter range that is set then the subject will not be in focus.
This is particularly relevant if using the E-M1X subject detection which needs CAF+TR. I often use the focus limiter to speed up focusing with the bird subject detection and have now needed to turn on the beep to confirm focus after I realised that the tracking green square appeared yet the bird was unfocused. Looking for the little green focus dot whilst keeping the bird under the focus point is beyond me! 
You can test this yourself by setting the focus limiter to say 8m-100m and trying to focus on something a couple of meters away. CAF should not focus yet when CAF+TR is turned on the green tracking square appears when the shutter is half pressed even though the subject is still unfocussed.
Hope this may be of interest to someone.