The DeeZee Aluminum Headache Rack with Sliding Load Stops, part # DZ95050RB, has aluminum brackets.
As for modifying the headache rack, you can certainly do that. Most anything can be cut/welded to suit your needs. Of course, this will void your warranty as you said, and there is no guarantee it will work or perform they way it is designed to. In other words, you can but it's risky so I can't recommend doing it. view full answer...
According to my contact at B & W, their # BWPUCP7540BA headache rack uses 6-1/2 x 2-1/4 inch grommet mount taillights, which could be referred to as a 'standard' item. view full answer...
I spoke with my contact and B&W and the Custom Headache Rack # BWPUCP7500WA is made of 10 gauge steel except for the flat plates that attach to the bed sides. Those are 7 gauge.
This rack is not tested with toolboxes or tonneau covers so it is difficult to determine if it will work in conjunction with those items. It likely will not work if the tonneau cover blocks the lip in the inner part of the bed sides. view full answer...