This is even true with the GM HD hoods. I picked mine, like many other guys, directly off a parted out 2002 Chevy Silverado HD. It fits directly to the 6 bolts holes on the hinges, however the fender to hood gap is noticeably spread wider. Maybe a millimeter or two (+/-).
But it fits at the cowl, the grille and the lights as well. There is tiny gap between the hood and the black rubber spacers. There is just something about the seams and if you read the many HD threads, you will see this is well discussed. Some fit better than others, however there isn't really much to adjust (without starting to push in on body panels, etc...). as you only have 6 bolts. I have looked at HD Silverados driving down the road and noticed that the seams are a bit wider than non HD trucks or our NBS models.
I took it to a custom hot rod shop and chatted with the owner. We looked at the fender to door gap and fender to bumper and grille gaps. Everything was lined up as good as they lined up for the NBS and we all know that they are not super tight to begin with all around the truck.
He said sure we could ram on the fenders and maybe ream out and epoxy some new holes for the fenders or hinges, if I really wanted to go that absolute with fitment, but then you risk misalignment of the doors, etc...
In his eyes, he said, this isn't that bad. If you can deal with what only those who know about this mod would care about and knowing that the average Joe would never notice then roll with it.
I still would't ditch it for a small imperfection on a unicorn mod. My .02.