General,
Yes, mine is just below 3/8" from the rear front fender, door and the bed.
I see what you mean by the front fender cup trim on mine and others.
NorCalC20LWB's trucks lower trim looks beautiful hugging that line.
I'm far from an expert but I think following the body line slightly below or follows on it, you're good to go!
You may be right, it may be a factory assembly difference.
As long as your cab mounts and bed lines are leveled correctly I think you're fine.
Good luck!