I hate to suggest you're being too picky, but I think you're being too picky.

Seriously though, the gap on the hood I can see being addressed. Hell, now that I've noticed it on my wife's car, I might adjust it as well. Pretty simple since it's not a big variance and will probably resolve with just a minor change in the stop height. ....but it really depends because by lowering the height at the gap, you could be lowering the height between the hood and the fender on that side. I've had cars with similar gaps that once you adjusted the bump stop, the hood was no longer level with the fender. On these cars it's not as big a deal because the gap is on the horizontal side of the fender.
I'm sure there is an allowance and expectation for variances like that in the manufacturing process. I'm sure I could go over your car, my car and even my wife's car and find similar variances in the trim, lights, molding, panels, etc. In fact, I already have on my own and in some cases, made adjustments (the trunk lid and tail lights had similar issues which I corrected). In that case, it required adjusting the stops but also some physical "coaxing" of components to get them more in alignment which is what you sometimes have to do. On the Challengers the taillights didn't always line up with the trunk lid closed. The difference was relatively minor on mine and correctable.
....but the alignment of the hood by the cowl, while being something that may be able to be adjusted might be better left alone. I honestly don't think you want to go down that rabbit hole as that will likely involve the adjustment of the hood at the hinges that may result in variances elsewhere. That can be a lot of fiddling I'm not sure a dealer will be willing to spend time doing for something that is literally just a millimeter or two off.
....but that's just my two cents and I wouldn't want to suggest you accept something you don't feel you should.
btw, I was quite a bit more picky than I am now so believe me when I say that I understand. Even today I still notice things like you describe. I can't tell you how many times I immediately noticed things on other peoples cars that they had no idea were there (e.g. flaws, inconsistencies, past repairs they knew nothing about, etc.). My eyes are simply drawn to them. It wasn't until the last decade or so I learned to tune out some of that stuff when I want to. ....and it's not always easy.
In fact, I had a similar issue with the wife's car on the back bumper. I noticed a small imperfection in the paint from the factory. It appears to be a possible contaminant that splattered in a small area prior to painting. I'm not too worried about since it's plastic, there is no risk of corrosion underneath and it's in an inconspicuous spot. I didn't even catch it until we brought the car home and applied a sealant the next week. ....but I also don't want to address it with the dealer because a repaint will likely cause more irregularities than it corrects and potential issue down the road if it's not done right.
The funny thing is, I debated showing my wife because I know she would probably never, ever notice. ....but I did anyhow.

What I'll end up doing is using my past detailing experience, tools and products to try and correct that area as best I can. I'm confident I can improve the appearance of the imperfection a bit. As for my wife, she simply asked me if it would be a problem down the line (paint failure), I said I doubt it and now I doubt she will ever remember it again unless I point it out.
