Are they only good with the specific disc they came with?
Say my original disc from Gamestop (flight suit) gets scratched… I buy another one from Best Buy (Ghoul) or Walmart (gold proton pack).
Do I get to keep the flight suit that i did pay for?
If so, would that then make it possible to overlap all 3 codes by buying 3 different copies, and have a ghoul in the gray flight suit sporting a gold proton pack?
Why in the hell am I thinking about this this time of night?
More than likely, as the disc itself doesn’t determine what preorder bonus you get…the code you use does that. The preorder bonuses come in the form of PlayStation Store or Xbox Live Marketplace downloads. They’re not actually stored on the disc.
The disc has nothing to do with the codes themselves. The disc you received in your GameStop case with your flight suit code is the exact same disc that is packaged with the Wal*mart and BestBuy ones as well as the generic ones without codes.
The codes when redeemed are downloaded to your hard drive and regardless as the disc will remain on your hard drive.
Hope that helps 
And yes you can use the codes together.I’ve used the GB2 suit with the Gold proton pack.
If you want to get technical, all of the data for the items ARE stored on the disk, Otherwise they wouldn’t be compatible with the items. Part of the data are on the disk (taking up an extremely minimal amount of space) while the other part is from the download code. If it wasn’t - other players wouldn’t be able to see the Zombie/GB2 Suit/Gold Pack in multiplayer.
The same idea went with Street Fighter 4 and the alternate costumes. If the data wasn’t stored on the disk, I wouldn’t be fighting against a Battle-Damaged Ryu.