I'm not absolutely certain, but I believe the Boxed DVD is just that, a standard DVD 5.25" X 7.5" black or clear storage case with perhaps a little information booklet or sheet of instructions inside.
Download plus DVD might mean you D/L it and, in addition, they burn and send you a backup DVD they make on site at the store, slipped into a paper or plastic envelope of the same size as the DVD and then mailed to you.
Shouldn't be any difference in the content of either, I prefer full box editions for larger sized products, scenery in particular because of the size (GB's). Plus the DVD cases are easier to store and find when I need to. The backup discs I have tend to run off to that place where all the coat hangers go never to be seen again.