It's as simple as this, Atlus scratches the back of brick n' mortar and online retailers and they scratch back. In return for the store-specific DLC Gamestop will likely promote Shin Megami Tensei IV; provide it more shelf space or simply more prominent shelf space, advertise it in store, up-sell the game, etc. Atlus is just playing the same terrible game that most other major publishers engage in to help their game at retail.
I pre-ordered it at EB today when I went to pick up my copy of Soul Hackers, not because I want that nasty costume, just because I want that first print-run goodness.