Bare bed-rail & underside of bed rail cap. 2011 5.5' bed

 

I bet a router with a flush trim bit would do an excellent job. Just make sure that the cap can't move around when you're doing the routing.

 

In regards to the structural strength of the short bed, versus the 6.5, it would be the same or stronger. Everything being equal, a shorter piece of steel will have more rigidity that a longer piece. Just simple science. Leaving the stake pockets out is just a pain in the @$$ stupid mistake by Ford.