Yes, you can make cutouts as seen in the image I posted above (the red control board). I've done it a few times, however for some reason when uploaded the design to jlcpcb the cutout area is not shown. After asking tech support they said it will be cut.
You can draw a square, rectangle or circle using the pink/purple board outline drawing tool. Or you can create a square/rectangle from the "pcb tools" menu, then right click the solid shape and choose " convert to board cutout".
I've done it both ways.