AFIAK, it applies in all modes including custom modes. When I change or turn off/on the adjustment, in a regular mode (Av, etc.), the change is reflected in all 3 custom modes, and vice versa.
In fact, AFMA is a bit pernicious - if you reset the camera to default, it returns the main AFMA setting to default (0: no adjustment), but it doesn't delete the lens-specific adjustments previously stored. The only way to delete an adjustment is to set it to zero with the lens attached, or when you get to 20 stored. (I wonder if the 1D X will store more adjustments?)