Probably because...
(1) It would make any current body illegal since they won't have a clear spot to measure... that was one of the beefs people made and was considered in the final rule configuration.
(2) The measurement can be taken anywhere in the general area designated so a small spot steers the inspection to a particular spot .
(3) From what I have measured on my own bodies, the paint will only add about a thousandth of an inch... who really wants to add a lot of paint? Most guys barely have enough to make it opaque as it is .
(4) If i'm not mistaken, a "normal" amount of paint was taken into consideration.
You can beat this to death six ways to Sunday...