It was definitely optional when I got my permit a few years ago.
However, most people I knew paid it - it wasn't just an exit fee, it enabled you to re-enter at Whitney Portal. Realistically, most thru-hikers exiting at a point are going to re-enter at the same point, so it was necessary and not a mistake.
Since most thru-hikers apply for their permits several months before hitting Whitney, it was safest to tick the box, just in case you did need to resupply at that point.
The 1,400 permits include long section hikes - my guess would be that perhaps half of those are thru-hikes, of which maybe half ticked the Whitney box, so 350x$15=$5250.
