When talking to the linex in anaheim california, "over/under the rails" was explained to me as having nothing to do with the deck rail system; instead, its the top of the sides of the bed. In other words,if you were on standing next to your truck, and rested your arms on the sides of the bed (so your arms are parallel to the ground), the portion of the bed that your arms are resting on is the "rails". I hope this makes sense; I'm getting a headache trying to correctly describe what I'm picturing in my head...
So, if your use of the truck includes scenarios where you're abusing these rails, then going over the rails would probably be a good idea.
Hope this helps...