The door is a little shorter than the frame so it can be opened with the top down - the frame actually extends up to the top of the sidewall which is under the lip of the cap, so they should not align.
Now the gap on yours looks a bit wider than ours, our weatherstrip would rub the edge of the cap, but some gap should be there. There should be a weatherstrip on the top of the door that keeps water out. We never had any water infiltration with ours.
ETA: the next item on eBay after maromeo's link is the door topper seal: http://www.ebay.com/itm/JAYCO-DOOR-S...3D141469682849