Explodium

This is just a thought, but maybe it could be a media review copy (IGN, GameSpot, etc)? Having a standardized spine for different games could make sense in that application but idk. Trying to think of any situation where it might make sense to have a different version that would be so rare that less than a handful have cropped up in almost 2 decades.

3 minutes ago, RH said:

This might be a long shot, but maybe what's happening is that these inserts are created using a special tool that needs an image per section-- a front image, back image and a spine image.  Nintendo might use those first and third party images to then "build" the final image that's printed, by properly applying the top overlay on the front, and the bottom overlays on the side and back, all of which as standard.

Now, if there was some type of print error, maybe the printer would default the name of the game, or something on the back.  Sort of place holders.  I highly doubt any botched printings of the front or back would slip past QA, but I could definitely see a semi-formalized side label getting past QA for a batch or two.  However, once the print was noticed, it might have been halted, re-printed and then production might have continued.  In that case,  who knows, maybe only a few cases of both games went out the door this way.

The fact that these were both at E3 is interesting, but if this has a registration card, it definitely makes it seem like it was an official release.  I have no clue what's going on, but this is my best guess and would kind of make sense.

Its more complicated that that unfortunately. Take a close look at the ESRB logos, the black spine one is closer to the E in sunshine. Also the grey lines that radiate out from the center on the normal copy fade to white near the center, on the black spine copy they are much more visible. Also the black spine one's pre-owned sticker is dated 12/20/03, a few months after the Player Choice copy was released. If you look at a normal PC copy the ESRB logo is closer but not in the exact same spot. So the cover was likely not from the same file used to print normal copies or PC copies. I really really wish I could closely inspect that copy of Metroid Prime. 

13 minutes ago, 0xDEAFC0DE said:

What does the code read that is above the UPC and to the right of the Dolby logo. The one that starts as "DOL P..."

DOL P GMSE, same as normal copy. All text is exactly the same on both copies as far as I can see. Here is a comparison of my two copies.

Could be worth noting that Metroid Prime and SMSS were both showcased at 2002s E3

https://www.giantbomb.com/e3-2002/3015-3434/

Seeing as the only clue to go off of is the lettering itself, I decided to do a reverse search of the text. The font used appears to be Serpentine sans regular https://www.fontsplace.com/serpentine-sans-icg-free-font-download.html

Edit: dead end, but the font does look familiar to me, I cant quite place it though...

Here is something interesting but not terribly helpful; Pricecharting.com has the only picture I could find on the internet of my copy of sunshine

https://www.pricecharting.com/game/gamecube/super-mario-sunshine

Look familiar? Same font and everything. I found this today at my local flea market, sadly disc missing. However, the registration card was with it which makes me doubt its some kind of bootleg. I also no nothing definitive about this version aside from the fact that apparently Metroid Prime also has a "black spine" variant...  Edit: the UPC code is the same as my normal copy of sunshine.