The ad on the aftermarket retractable running boards looks like they use electric window motors to do the work, so two would probably be a bit easier to maintain, should be a lot less linkage to bind up in harsh conditions.

As far as protection from parking lot idiots, I have to wonder if the retractable boards, when lowered, may be too low to be very effective for that. On a lot of modern car doors, the bottom of the doors curve in a lot, and most of the back doors have the wheel cutout on the outside edge. If no part of the running board makes contact with the idiot's car door before it can cause damage to the side of the truck, it won't offer much protection. The standard issue running boards are 3" to 4" higher (maybe more) then the retractable boards in the down position, that puts the running board at a better position to catch the idiot's car door. It may be such a thing that the retractable board in the retracted position (up) extends out far enough past the rockers to be pretty effective when in the up position.
Food for thought. Gene