Again it is not a "misalignment"!
Actually, looking at the photos you posted, it is a misalignment. I see what you're saying about the "dimple", but that wouldn't really bug me that much. It doesn't really look all that out of place. What would drive me crazy is the obvious misalignment. Look at the "break points" between the silver trim and the black parts of the door panel. Now look where the door meets the dash at those points. There is an obvious vertical misalignment, of the horizontal seams/break points. It also looks like the gap between the door panel and the dash is not consistent from top to bottom.
I think you are 100% correct that ford should fix it. Its still under warranty, and this is clearly a manufacturing defect. Regardless of whether it affects safety or not (which it doesn't), it still ought to be right, and if not, you have a right to have it fixed. You could try suing them. It make more sense to do so in small claims court. Its unlikely they (Ford) would even show up, and you would win a default judgement. Then, their legal dept. would probably just pay it upon presentation. Granted, it might not be much (small claims are usually limited to $2,000-$5,000 depending on jurisdiction), but it would be a moral victory, plus it would help cover some of the depreciation you are experiencing.
For those of you saying you are just "living with it" on your vehicle, you are part of the problem. Letting Ford get away with it, and not making the biggest stink you can lets them feel "safe" ignoring the few people who do have the guts to hold them (Ford) to the standard they were paid to deliver. If all affected owners raised hell, Ford would not be able to ignore it. Is it a Mercedes? NO. But it costs nearly as much, and there is absolutely no excuse for sloppy manufacturing/panel fit and finish on a $40-$50k vehicle, period. If it were a $15-$20k economy car, maybe you live with some cosmetic imperfections, but not a vehicle of this price range. As far as I'm concerned, Ford owes this guy (and every other affected owner) a properly made manufactured and installed door panel(s), period. If they have to scrap 20K "bad" ones and and have them made by another vendor, too bad. That's what they have to do. If Ford has to spend 10 million dollars, and the CEO loses his annual bonus, oh well. They made the problem, its on them to fix it, no matter the cost or inconvenience. Its called having honesty and integrity, something sorely lacking in much of society today, especially among big companies.
Another option, although a long shot, is to see if you can make a even halfway credible claim that this defect in the panel affects either the seal of the door to the outside, and/or the duct work routing defrost air from the dash into the door. If so, it becomes more then a cosmetic flaw. It now becomes an issue affecting a major mechanical system (HVAC), the malfunction of which could substantially impede your use/enjoyment of the vehicle as designed/purchased. Then, it opens up the possibility of a lemon law claim, depending on your state laws. You've already brought it in at least twice (from the sound of your post) for the same problem. Most states, is 3 strikes and they're out. If the manufacturer can't fix a significant defect in 3 attempts, they have to buy the car back from you. It might be something worth looking into, if you really want out of it, without having to take a major hit on re-sale (which you shouldn't have to if they sold you a defective vehicle). Again, that would all hinge on proving it is more then just cosmetic, but actually affects a mechanical system, and/or substantially impedes your full usage/enjoyment of the vehicle. This is probably a long shot though.
Anyway, this is just another reason why I would never buy a new car. Total waste of money. Might as well buy used, after someone else has gotten the problems sorted out, and taken the huge hit on the depreciation.
The only reason I would consider it is to get the EXACT vehicle I wanted. The only way that would be possible is if I had enough money, and clout, to run roughshod over the dealer and/or the regional sales people with Ford, to basically force them into building what I want, not what they want to sell, in terms of options, tweaks, disabling "mandatory" "nanny" garbage, etc... Think Jay Leno, or maybe Bill Gates walking in and demanding the car they want, built exactly to their specs. Otherwise, it isn't worth it.