I use the square Thule bar system, with their lock-able upright supports that you can slide into place anywhere on the bars that you need[kind of "D' shapped, with a screw handle at their bottom to clamp under a bar tightly]. I use 4 of these supports, and have carried up to 4 sheets of 4/8" plywood at a time or 4x4 landscaping timber when I needed to bring home under a dozen for a backyard project. That being said, I hate carrying any weight on the roof since you get so top heavy as a result. Aluminum racks are nice, lighter than steel and don't rust, but you need a welder that can handle them.
Maybe just use roof bars and weld or bolt up a steel basket system to span between the two bars.
Are you looking for long range trekking like desert driving or camping as well as hauling building supplies?. This could change your design a bit, just remember the pros and cons of a permanently mounted roof system.