According to this site ... http://www.friktech.com/btls/covers.htm
... the trunk cover was actually meant to be the original cover and several proof designs were made up.
But then the Beatles saw the butcher photos and chose one of those for the cover instead.
Later, when the butcher covers were recalled, a new trunk cover was hastily assembled.
Interestingly, all known cover designs have the trunk cover reversed. Perhaps it was because the original background of that photo has a light area in the top right (when reversed) which was ideal for placement of the Capitol logo at the top right of the sleeve. Had it not been reversed the photo would have had a darker area up at the top right corner which could have masked the Capitol logo. That's just my speculation, of course. I doubt we'll ever know for sure.