I suspect (and again, this is just my opinion) that to a large degree it has to do with people submitting for certificates who have not hiked the entire trail. I've met an awful lot of people in WV, MD, and PA who will freely admit to skipping sections in Virginia and are still comfortable with referring to what they're doing as a thru-hike and themselves as thru-hikers. I suspect these folks are equally comfortable with submitting their hikes to ATC as thru-hikes.