The issue is not so much getting it lined up properly, but rather ensuring that the print process creates artwork that is scaled exactly so that 1" on your program/file = 1" on the print. With a cut before print method, your print can't have any errors in scaling at all. For instance, if it only prints 0.01" 'bigger' per inch (IOW if you have a 1" diam circle in the file, and the print makes the circle 1.01" diam) that doesn't sound bad until you add up the error across the print, and that 0.01" error ends up being 1/4" off at the other end of a 25" CPO. If you have any button outlines or text or whatever that keys into the position of the button (and thus hole), it would be very noticable. Especially if it's a printed ring around the button, or say a button 'halo'.
If you do the print first (and/or get the drill plot), then you take this variability out of the equation. Getting a drill plot from the same printer would ensure that any scaling effects/issues that the printer may have will be the same from the plot to the art. This means that even though your file may say the distance between two holes is (say) 20.50", and the printer prints 0.01" per inch bigger, then the distance on the print would be 20.705". If you drill first to the 20.50" spec, you'd be 0.205" off. If you get the drill plot from the same printer, then it would show the holes as being 20.705" apart. Drill to that, and then the art matches. Then use the light method to line it up if you desire.
Good luck,
Rick