Boxes are better for multiple reasons, but cost also matters. It depends on how much skiing you actually do and how much other uses you have for whatever you purchase. My ski box probably costs about 1 MPG on average. In the end, if such a miniscule difference is a big concern I'd hate to think how much you fret over other decisions hahaha. Loss of a little gas mileage is a very small price to pay for the pleasure of getting to ski.
If you're really are trying to be frugal and keep your costs down I can relate. Think of it this way. You probably saved about $400 by purchasing a rack instead of a box. I'd still be using a rack if I hadn't found my ski box on Craigslist for $50.00 Dropping $500 on something I don't use while actually skiing, even something that useful, just hasn't ever been in my ski budget..