So to answer some questions:
I've had this in for 6 months. I don't usually carry the jack unless I absolutely need to. So really, the 2 mounting brackets haven't been an issue at all as far as putting stuff back there.
Hi-Lift sells a lift-mate that attaches to the jack and can lift the wheel up on one side attached by 2 points. Helps with our plastic sides.
I do have a roof rack, but the reason I choose this location instead, was logistically, the roof was harder to get to. The jack has some weight to it and to get it up on the roof meant I had to use the side steps and if they were slippery at all (which could happen if your standing in mud), I could easily see the jack going through a window.
Besides, I also want to retain the stock look of the truck as much as possible.