I agree that the punches are effectively the same. They are merely a means to an end. Whatever technique you use, if it leaves the opponent on the floor and you still standing, it's a good technique.
I disagree with you, however, on the point that distances affect the punch. Unless a punch is fully extended, it does not transfer your body's momentum and relies on less powerful muscle strength for effect.
I believe that the index and middle knuckles are more structurally sound for punching hard surfaces where as the outer knuckles are more effective for impacting soft surfaces. The reason being that the outer knuckles tend to be used on stronger punches (e.g. hook) but can take damage in the form of the Boxer's Fracture. The index an middle knuckles are not the primary knuckles which are broken on punching a hard target but are used in less powerful punches (straight and twist punches).
Don't try to fit a square peg into a round hole. Use each technique for what it's good for.