I am confused, do you want to weld the holes up because you don't need them (not going to run fenders) or do you want to not have bolts showing in the inside of the bed?
There is NO way you are going to weld those holes up with a "stud" sticking out to mount the fender without showing a horrible "dent" on the inside once the nut is tightened.
What exactly are you after?
Brian