It's real (at least the pictures are of a real Supreme). I have a twin made in 2008.
The case has an extra latch
The shroud is not attached to the case.
The frets are gold (not real gold - just the color)
If it were me, I would return it. If it bothers you enough to post about it, then it is always going to bother you. That looks like one of those hard to replace, expensive cases too.
If it was my case, I wouldn't have asked. I would have already had them replace it.
I'd be willing to bet that is a 2009. I have the same guitar. The bonus is that it has an ebony fret board. I don't think they were making Silverburst Studios in 2003 but I could be wrong. Here is a picture of mine:
Same Grover tuners. Reflectors. Rimburst too. My money is on 2009.
It is another attempt at the Gibson PAF pickups with AlNiCo 3 magnets. Some people like them, some people hate them. I don't have a guitar that has these pickups, but I've heard they are a little lower output. They usually put them in Reissue guitars.
Wow! You are lucky that you got all that when you purchased from Guitar Center. I've purchased MANY guitars from them over the years and they have a tendency to swipe everything out of the case (or give you the wrong case). I've been in many arguments over the years with them about this very...