I usually use the "middle" option. (Placing the door over the jigsaw, without an endcap.)
I get the aesthetics of putting an endcap there, but I feel like it would just be adding that much more wear and tear to the jigsaw bits to put an endcap on and then remove it again. Not to mention the risk of disturbing the board while removing it. I might feel differently if I had problems with the door falling over or something, but that's never been an issue.