If you're lucky (and your board house supports it), you might be able to sneak your fiducial into the footprint too - right at the corner of the board, and not taking up precious space. Check to be sure that there's enough free space around the fiducial - my PnP and solderpaste machines are happy with this, but others may need more clearance. Worth a try, though, especially on a tightly packed board.
Edit: The fiducial isn't part of the hole footprint, it's a standalone part, to make sure it appears correctly on the pick & place data with a location.