For the record, this was intentional, as the large Link sprite was intended for overhead view, as Z3 or MC. The hitbox area was designed to be his feet, to collide with Solid Damage Combos, and such, so that the upper-portion was not generating exztra damage, or causing overlap problems with solid combos, and such.
If we properly add Link->Extend, and fix the other attribs tied to it (e.g. HitWidth, HitXOffset), we should be able to fit custom hitboxes for Link in a future build. I looked at the code, and there's nothing that really makes any relationship with these values to the actual hit detection. We'd need to add that, and do a partial rewrite of the collision code to support it.
Another thing we might be able to do as a stopgap, is change the hitbox for Large Link in SideView mode. That might be more straightforward, and would allow sidescrollers to use the large sprite with fewer bugs.
