Hadn't noticed this before:

When a huge ship executes a maneuver and the final position of one of its sections overlaps one or more small or large ships, the small or large ships overlapped by the huge ship are immediately destroyed and the huge ship completes its maneuver.

The huge ship does not skip its “Perform Action” step. Then, the huge ship’s player rolls one attack die for each small ship destroyed in the overlap and two attack dice for each large ship destroyed in the overlap. Then the huge ship’s fore section suffers any damage and critical damage rolled.

So even if the Aft section overlaps and destroys the ship, it's still the Fore section that takes any damage incurred.

Seems clear enough but an odd way to resolve it

It is a little weird, especially since (if I remember right) huge-on-huge and huge-on-obstacle collisions inflict damage on the specific section that collided. I'm not sure why they resolve that case differently. Maybe so there's never a situation where you have to hold your huge ship over the smaller ship to figure out which base overlapped it? That could lead to some pretty tragic accidents.

It makes sense for the front of a huge ship to take the damage when running into a smaller ship and destroying it. This is the key things here because while the back of the ship may 'stop' where the little ship was in most cases the front end would have had to go over it first. I'll admit that the fish-tail turn could kick the back out enough to land on something but how often is that the case and perhaps the front moved into there to start with to start making the corner.