This is simply build variation - and it's a consequence of the "stackup" of the dimensional variations (within tolerance bandwidth) of all of the components involved, the net effects of welding, etc. etc. "Sloppiness" is likely not a factor, since these parts are likely designed to "mate" together and you get what you get once that's done.
Is it "normal?" Well, it might be outside of the specified tolerance range. It's clearly bothersome to you, it's noticeable, and that's all that matters.
Of course, If there are wind and/or water leaks, or even just related wind noise, that would clearly violate specifications for the vehicle. These would absolutely be covered under the warranty.
Its worth a quick check of the roof panel itself compared to another. It seems doubtful though, owing to the nature of the tooling for the panel, that it would be that far out.
I'd have the dealership remove the roof panel (bolted connections) and carefully refit it. Perhaps there is indeed some "slop" in the fit that would allow this condition to be adjusted out. However, it is possible that it
might not be a condition that can be easily improved, since the interface locations are dictated by where they ended up on the body structure itself. In such a case, the body would have to be "tweaked" to bring these locations back to where they should be. Most dealerships wouldn't be competent, in my estimation, to do this correctly.
The seals are designed to take up this type of variation. If it doesn't leak or make noise, I'd live with it. Doesn't look great, I admit. But the car will drive just fine either way - thankfully. :cool:
I'd be annoyed too.
Another LS engine comin' up. 
Linear Mode
