I think most aftermarket covers, hard or soft, are designed to fit without modifying the truck.
I think some of the soft covers are lockable. I looked into them a bit when I bought my '02 two years ago. Instead, I put a toolbox across the front and built a homemade plywood cover based on the one in the projects section here. I liked the toolbox, but then I found a topper/shell for it last May. I don't see that coming off any time soon. At the same time the topper showed up on craigslist, there was also an aftermarket full length hard cover for sale, and I bought it a few weeks later. I may never use it, but the price was right, and it matches my truck. I bought my '01 last spring, and it has a full length aftermarket hard cover on it. That one is taller than most and sits 3 1/2 to 4" above the box, where the one for the '02 is flat. I like both the topper and the hard cover, but I have trailers for the bigger things.