The difference with those titles are they expected to sell well and companies are offering gift cards because of competition and/or the game companies are subsidizing some of it (Doubt it). I believe Wal-Mart.com started the GC/promo war recently and Amazon started the first war years ago.
Basically Best Buy wants you to go to their store and buy other shit outside of the game (hence a gift card) and hope to make a few $ in profit when all is said and done. Amazon wants you to buy more shit to. Being a CAG we are somewhat evil if we don't "'overspend"' on Amazon products after getting promo credit and up just spending what we get in Amazon promo credit alone.
Why incentivize something that's going to sell well already? My issue is that I perceive retailers are using the same method (gift cards/credit) based on different expectations for each game and conditions within the market. Without having the information that retailers/publishers have that they base their expectations on, it difficult for me to attribute why X game is getting an incentive while game Y is getting is getting one as well. That's where my confusion of not seeing a difference stems from.
As far as publishers subsidizing these incentives, if this article is believed to be true, I can't see retailers forfeiting most/all of their margin. There has to be some kickback from the publishers if a retailer buys some amount of a title.