Remember... the images (pads, smd pads, solder mask openings, etc.) that are in each gerber file represent what will physically be part of the fabricated board. The hole is not a "feature" that will be etched etc..
What I do is add a line, with a width, that represents the outline of the cutout on the same layer that I have my board outline. Then I create an additional gerber file with only that layer turned on and send that gerber file to the board house along with the other gerber and drill files. I name that gerber file "Outline/Cutouts".