I like to keep boxes for a few reasons - if they have a nice design, to keep accessories in a place i'll remember, and for the few times i have to transport pricier figures or figures that could get damaged easily if not in a fitting plastic prison

That said, i don't think i would pay the extra amount you did, perhaps my limit would be something like $10 extra, or if there was some question as to the nature of the loose toy (knockoff or factory reject etc)