I also find interesting, is when a flag ship levels. If the ship is at full hit points when it levels the new hit points are added and the ship is at max full 'new' hit points. But if the ship is damaged when it levels, the max possible hit points is raised to the new level, but the ship stays at the previous damaged number of hit points.

I would think the behavior would be both one way (add the net new hit point always) or another (never add to the current level of hit points but just raise the max and let them repair to full).