I went with the Bakflip F1. I struggled with the same things you are. It really came down to price for me. I was getting the cover and the box from both of these companies but I was able to get the Bakflip and box for about $300 less than the fold-a-cover even with their specials. One could say you get what you pay for I guess because I question the durability of the box. The cover on the other hand I have had great success with the HD cover for 5 years before now.
I looked at the BakFlip and the Undercover. I found them both very similar and went with the Undercover simply because it saved a few bucks. Very pleased with it. Easy install, have used it in its various positions with no trouble. Good luck with your choice.