Sstock,
I home built my bed and rear cross member. I did not weld it together and I painted under the stake pocket before spot welding. I assembled the bed and painted it as a unit. The rear bolts of the tailgate trunnions and tail light brackets hold it square by tightness. This being said however, my rear cross sill is made out of 2x6 tubing with 1/8" walls and nuts welded inside the tube, so it's VERY solid compared to original.
I suspect if you tried to use brute force tightening the bolts on a stock rear crossmember to hold the bed square that you would create dents in it.
