I just did the AFMA on my 5DIII (firmware 1.1.3) with a 70-200 f/2.8L IS II and a 1.4x III, using FoCal Professional, version 1.6.
Like neuro, I have found it registers as a unique combination.
In fact on the 5D mark III, you can register by the lens and TC serial numbers as well - so the AFMA settings are set for Tele and Wide for each lens/combination.
By way of example, my lens AFMA's look like this:
70-200 f/2.8L IS II : AFMA @ 70 = 0, AFMA @ 200 = 2
70-200 f/2.8L IS II + 1.4x III 98 (70 * 1.4) = -1. AFMA @ 280 (200 * 1.4) = 4
I had forgotten the need to perform AFMA on the lens/TC combination - when shooting a cricket match recently, I found that there was front-focus when using the 1.4x III that wasn't there using the bare 200 lens.