It looks to me that some of those fishing boats are using the set back distance to create deck space for stepping around while reeling in the catch of the day - no splash well to slip into inadvertently, or any cabling to trip on.
For boats that are rated with a motor mounted on the transom, a set back would create additional stress, as the mounting bolts turn into a fulcrum point with the weight distributed further away (generates a moment force), like adding an extension to your socket wrench.