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I have a deep style over the rail toolbox on a short bed. I needed the toolbox capacity and that was the only real option. An under rail box looks cleaner, but wouldn't work for me.
Yes I have a cross over tool box, But it is more then just a tool. In the very front of the bed I have a diesel fuel tank and behind it the cross over extra deep tool box. I built a steel frame that mounts the two, but yet hold them off of the bed floor about 8 inches. This allows the full use of the bed for longer objects, like plywood. I use the tool box to store not only tools and hydraulic jack in case of repairs, but there is a Warn 6000 lb winch mounted in the center. I cut the side of the tool box large enough to mount the fair-lead, and only the hook is seen. We use it mostly to pull our quads in and out of the bed, but it has come in handy a few times for other large and heavy items. I to like the look and function of a tonneau cover, most times I just like to have things out of the view of others. I bought one and customized the front to attach to the tool box, and the rest fit as it normally would. I love it, you have the best of both worlds, easy to remove and I think looks nice.
I have a low profile over the rail box. I use it for my suitcases and tire chains when I travel. It is installed with camper shell mounting brackets so I didnt have to drill any holes. I can still put a full load under it. I have about 12 inches between it and the floor of the bed.
My box is in the bed. It is a Challenger. It works well for me and the way I use the truck. I miss the roll top in the winter especially when skiing. It was nice to keep skis and other equipment under cover. I also had the tailgate lock so things were somewhat secure. Since I am towing fivers a lot of the time I went with the tool box set up. It becomes a matter of preference and what you are using the truck for. I found a couple of tool boxes that I liked better than the one I have but they were above the box rails and would have interfered with the trailer in tight turns. The same would apply to a crossover box. Good luck.
I have been using a 36" challenger chest in the back of my last two trucks (same box just moved it). It has worked great leaves space on the sides to put small items such as gas cans and coolers , chainsaws etc etc and doesn't allow them to float around in the bed. It really depends on how much stuff you want/need to store in it. It also would allow the use of a cover. I have it mounted with 2 lag bolts through the bed floor with coarse threads. That holds it tight but also makes it very easy to remove in less than two minutes if needed. I have been rearended a couple times with it and it has held fast. With that being said I have found that after 8 years of using it I have decided that I need more storage space and have decided on a delta pro single lid deep box.
I also recently ran across a company called Tuffy something or other that had boxes that were side boxes that went from front to rear and went over the wheel wells and flush with the bed rail but full depth in front and behind the wells sort of a neat idea I thought. They used pretty much unusable space as opposed to a regular box.
an aluminum over the bedrail tool box in mine. In my application (gooseneck trailers) a bed cover won't work. I have one that has a single door that can be opened from either side, rather than a door on each side which gives me better access (likely to put anything in a toolbox).
One thought. I will never get an aluminum toolbox again. After a little use, everything in it is covered with aluminum dust... and you end up getting it on everything! Didn't think about this when I bought it. Talked to one of the locals about doing a spray-in liner for it... wanted $150+. Needless to say, it has not been done.
Pro-Tech aluminum cross over on the rails. Tonneau is by no means water proof and not near tough enough for my abuse. Also not an option due to goosnecks.
About $500 for a toolbox (admittedly not a giant one, but I have a short box) and tilting tonno cover. I love mine. The tonno is even designed to fit inside the toolbox during shipping so it won't get damaged.
I have a Weatherguard over the rails DEEP diamond plate box that I have used in two other trucks before this one. This box has taken an extreme amount of abuse in the past five years and looks almost as good as new today as it did when new. These are well constructed boxes.