I did the BED RAILS as well, and really love them...I used a box cutter, and ended up with better edges than the Dremel, but yes, it doesn't matter, it's all covered up. I also prefer the look of the rails, as I've always thought the profile of the truck was a hair out of balance.
The downside of the rails is I also have the BED EXTENDER, which has to be dis-attached and flipped depending on if I want it inward or outward. It's super easy to do, just a little awkward. The Bed Extender is probably my favorite add on, as cargo (groceries, kids backpacks, etc.) doesn't shift to the bulkhead all the time.