I've drilled a couple of tour paks to match the holes in the tour pak to the detachable rack. Used painter's tape on the bottom of the tour pak; found and marked the centerline of the tour pak on the tape with a Sharpie; found marked centerline of the rack; matched the centerlines of the tour pak and rack; established fore/aft location of the rack on the tour pak; then used a high speed drill bit to drill the tour pak bottom; cleared the drill bit of the tour pak material; and, then drilled the metal plate.
The tour paks I drilled had holes already and the drilling was necessary because, in one case the tour pak was for an '08 bike and was being mounted on an '09 bike (the '09 rack has different hole dimensions than '08 and older tour paks), and the other tour pak was being mounted on an older version of the Milwaukee Bagger detachable rack that had non-HD hole locations.
Surprised that you can buy a HD tour pak, color-matched, that doesn't have the correct holes (or any holes according to the original post) for mounting on an HD detachable rack since the tour paks are listed by color and model year with the latter being included to provide the correct hole locations; e.g. there are multiple listings of tour paks in vivid black based on model year. If you received a new tour pak from HD with no holes, perhaps it's a production mistake.
Carl