For one thing, two Yamato boxes are bigger than one Yamato bundle (at least that is what I saw with the VF-1J set). You have to imagine to live in a room as small as me.
Next, the price might be cheaper. At least in some stores in japan, were the retail price means absolutely nothing to them.
And finally, there might be fixed and tweaks with a later release.
Also, with the girlfriend, you can pass a bundle as 1 buy instead of two...less explanation to do.