Well, without a box, you'll get grit from the road in your bindings, which might damage them. They may also cause abrasion and damage your setup. Also, if there is any snow/ice/water left on the bindings/skis, it will rust. A lot of problems if you ask me.
On the other hand, it will probably 'cause some loss in mileage, meaning you need to fill up more often ($$).
So, take your pick. Are you more passionate about your skis or your money?