Some of the alternate covers are used within the packaging of the other editions, i.e. the cover of the standard CD is inside the gatefold of the vinyl, the cover of the iTunes Deluxe Edition is on the booklet of the standard CD, etc.
The covers of the Japanese and Australian standard CDs are a variation on the cover of the US standard CD, with the painting oriented sideways and, in the case of the Japanese cover, photographed from a slightly different vantage pointand lighter in hue. The digital Audiophile Mastered Version cover is a variation on the standard digital cover, with the painting again oriented sideways.
In a post on the official NIN Tumblr account[http://nineinchnails.tumblr.com/post/55697135231/each-version-of-hesitation-marks-will-have-its-own], the various artwork was elaborated on by Mills: