The new store most likely isn't making a large profit on the pistol they were going to order for you. I would guess they would make $50-60 on the pistol if you bought it from them. They charge $25 for the FFL transfer that does not cost them anything but time and record keeping.

Either way, they are making money off of you. Buy some expensive bullets from them while you are there and you'll even out their profit margin on the whole deal.