[old Chevy guy]

I had that happen when I did my cab too. I think it's just poor stamping on the replacement part. If the door fits good and your lines are ok, nail it. Just check to Make sure your weatherstrip fits in the gap. As long as the weather strip gets in there the threshold piece will cover it all up and you won't see the discrepancies. That's what I think but I'm no body man, although I have repaired at least a half dozen of these cabs in the last 30 years.