swapping a box

I have come across a good deal on a possible, I say "possible" as it is off a 02, replacement box for my 99 kingcab 4x4. Aside from the tailgate and the huge fender flares it looks the same in pictures. Does anyone know if the bolt caps on the flares actually cover a bolt that goes into the fender? or is it just a cosmetic thing. I would want to put my origional ones on it but am not interested in filling in bolt holes that would be left in the fender.