It would be awesome to get extra attention on troublesome PCBs (and pay for it).
For example, I would like to make sure the production number doesn't get put on a part of the PCB that is used as a front panel (silkscreen on the back is often lower quality, and some PCBs are too complicated to flip sides.)
Other uses: First-timers who need handholding preparing gerbers; more accurate drills; difficult milling; etc...
yeah, its possible we might add a special instructions box and charge for it. In general though, I prefer to offer a completely standardized process to keep the price to a minimum.
Not printing it over pads would be a bonus :).