Door gap question

I'm fitting my door and fender and find that the fender has to be pushed in all the way and the door pulled out to get them fitting correctly. The back and bottom of the door looks good. As you can see there is a big difference in gaps at the top. The fender has about 0.1" gap for reference. I'm reluctant to let it go although fixing it means welding the top edge of the door up. I am just curious on your thoughts. Was this kind of flaw par for the course?

ps there is a small lump on the tip of the fender which I missed and need to remove.
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