I hadn't considered this, but that's a great observation. I'm going to stick with manual focus; hopefully the DR-6 will allow me to do that much faster.
AF is OK if you don't care about getting really sharp shots, and can shoot with a small aperture (f11 or even f16) so that the depth of field is wide enough to compensate for the AF errors. But if you really want sharp shots, you need to do manual focus.
I use f11 but if there is a scratch or two on the slab, AF will focus on them rather than the coin. The scratches will be much more prominent.
I shoot at f8 in order to help make any small scratch almost invisible. I have also found that f8 tends to give enough depth of field for almost any coin you want to shoot. That is assuming that your sensor plane, lens and coin surface are all perfectly lined up. I keep a small spirit level close by to double check everything on occasion.
I shoot Cents or smaller at f5.6 to maintain sharpness. DOF is just right long as the coin is perfectly flat. I use the mirror method to make sure. Dollars are OK for sharpness at f8 since magnification is lower.
The idea is to place a mirror where the coin goes; stop down the lens to increase depth of field; then adjust the focus until the front of the lens comes into reasonable focus. The center of the lens should be centered in the image. If not, you can make adjustments to the camera or bellows mount in order to center the lens and thus make the mirror (coin) and the sensor exactly parallel.