I have a fleetside, so I don't have running boards.
A buddy of mine picked this up last year. The inner bed panels are moved in a couple inches so the utility boxes are ~8" deep.
If I were more confident in my sheet metal abilities, I would love to do the same basic trick. Long bed, fleetside 58/59 beds are *hard* to come by. I am not willing to risk the one good one I have found to try and modify it.