Factory bed caps dirt traps?

[colstripguy]

I work at a coal fired powerplant lots of fine dust fine mud. Our shop pickup is a '10 F150. When we wash it, there is always lots of dirt under the factory bedrail /tailgate caps. It seems we never get it all out, no fenderwell liners. It looks like a great place for rust to start.
I have an '11 F250 on order,and I wanted to remove the caps and spray bedliner over the bedrails/tailgate to eliminate a place for the dirt/miosture to hide. The 2 vendors I talked to don't want to do this, as there are many goodsized holes that the caps clip into, making "soft", unsupported, spots in the srayon bedliner.
Has anyone noticed dirt/moisture accumulating under the factory caps?
Has anyone removed the factory caps, what did you do?
I live in southeast Montana, there aren't a lot of choices among vendors, so "just go someplace else" is a pretty limited option, the nearest major bedliner vendors are 90 to 300 miles away. Thanks, Pete

[mor4wd]

I work in the dust and I get a little dirt run out when I'm washing the truck but nothing too bad. Just have them line it and then get some countersunk bed tie down to put in the holes. It'll look good, especially if they're black.