I think we misunderstand each other here on some points. It is 6:30 Am here, so please forgive any spelling mistakes I will inevitably make.
First of all, I see what you mean with the "height of the sprite" thing, and that's where the confusion comes from. We both seem to understand how hitboxes actually work, as you stated with the math (I realize you kept it simple for the sake of convenience). You were talking about an increase of the character's
height, and I was talking about the sprite
height. These are not the same. The high heels in your example make it so the same hitboxes can not be used because your character actually needs to connect to the ground earlier. You will probably not see such changes in an alternate costume for that reason. It essentially like changing his posture, for all intents and purposes (regarding hitboxes).
In my example, I gave Luffy a quick alternate costume. Sleeves, boxing braces, a giant pointy hat, and a giant flowing cape. Bottom row shows the hitboxes. Completely different, if not silly (and pretty ugly, but as I mentioned, it's 6:30 and this is a rush job). The cape and hat are way out of the hitbox range, but they do not need to collide, as your character doesn't stand on them (floor-collision) or gets hurt when touched there, and vice-versa. Thus, the hitboxes can be recycled as usual. Our argument stemmed from the fact that you visualize costumes as something that could alter a character's height, whereas I see them as additions or changes that have no impact on the character itself. In those cases, and I take it those cases are the only viable ones, thus the only ones that the designers will use, the relative points do not change, thus the problem with the knife (as shown above) will not happen.