The healing process does impact your body; the scab will tug on the skin a bit, and there may be some inflammation. The itching/scratching sensation is your body’s sense of touching telling you something is wrong in that area. These two systems are working independently, so your sense of touch is just reacting to this tension on the skin.
It’s counterproductive, sure, but our bodies aren’t perfect. And if this isn’t posing a significant problem to our evolutionary purpose (to survive long enough to reproduce), then there won’t be any evolutionary pressure for this to change.
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