Which is why AFMA will not help you correct for focus shift at different apertures, as some certain pesky lenses seem to have (even expensive ones).
Still, we've gone from 1 AFMA value for a whole zoom lens to 2 values, long and wide end, and from per lens-type to per-serial-number.
In the future I don't see it impossible that you could dial in different values for different apertures too, it's just a matter of canon getting off their butts and coding it in (and maybe a bit more nvram for a huge lookup table), and a lot more work for us testing at every possible combination...