I think it's a question of exclusive vs. an assortment that is being carried by anyone who wants to order it from Hasbro. So all online retailers have it, all of the brick-and-mortar stores have it, etc... The volume of production and ordering for the BluRay sets is probably much higher than the Force Unleashed set. For the TFU set, I'd be inclined to believe that TRU ordered whatever the Minimum Order Quantity and that's it.
It's like that with everything. I get the clear stands from Marauder Inc. - if you get 25, I think it's like $0.35 a stand, if you get 50 it comes down to $0.30 and if you order 100 it's all the way down to roughly $0.25 a stand. Same thing is true with Star Cases from ProTech, the more you order the cheaper it is per unit.