Personally I like the flush, no hardware look of the bungees. I've used them on 5 of my yaks so far and the only major issue has been the flattening of the rear hatch on P1. This was my own fault as I used a piece of Okoume as a stiffener without scoring it so it would match the camber or the deck.
Yes, they may be a little hard to get into and I think require a bit more attention to the hatch edges that abrade the edge of the deck. I believe Nick uses 2oz glass on the edges.

Dan