Patch panels are generally made in China or other off shore place. Made from a die. The die is designed to fit a perfect truck. Generally the patch panels are all the same as the next batch except for die wear and handling. The USA made panels are not made with the kind of machines the Chinese have. They lean toward hand made. Probably from bucks and jigs. They are also made to a nominal original truck. Patch panels don't always fit perfectly due to things that happened to the truck over the years. Factory truck tolerances, patch panel tolerances, past "professional" collision repairs gone bad. Owner fixes, Frame and body sag/fatigue, other bad patch panels used. It's the nature of the beast. The patch panels from China do also get out of shape during the voyage, dock to vendors and shipping to you. It's one of them things. Patch panels give you an 80% head start vs fab.
To mitigate:
1. Don't cut anything til you get the panel and lay it on. Spend time thinking about it's fit.
2. Don't use any more of the patch than the truck needs.
3. Panels can be cut, modified, rebent, etc..tweaked.
4. Ask here before you start. You are experiencing what we all have experienced. So take two asprin and post in the morning.
The ideas from Kevin and the pie cut from Mark are examples of what may be needed for any patch, and are good advice. The first thing I thought is what kevin said. The gap has to be the number one thing to set up, then see what else is needed before cutting truck or patch. Cardboard can be used to test your ideas. I have used welding rod to reimagine a door edge, to close the gap. Probably not an idea for this however.
I don't know how much lip/flange length is on the patch where it meets the door, but some folks here could straighten that flange out and rebend it to the angle/distance needed. That is the opposite of letting that edge of the panel dictate. But it is a thought.