Just installed mine yesterday to pre-paint tub for test fitting. As TBP says, just put in the bolt and nut in the rear of the bracket and tighten it down snug. The bracket gives a bit allowing the bracket to bolt flat to the bed. The rail nut hits the floor but no problem since the bracket bolt snugs bracket down flat to the floor.
I guess I learned my lesson to just call when in doubt... Maybe one day I'll remove the washers to have more surface area touching the floor pan.