When you hold shift while flying, your eye level (the red line on the hitbox when you "F3 + B") is risen above the hitbox. (Hitbox Shrunken to small box when flying)
I am unable to post snapshots at the moment.
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Actually, that was the only way of getting them to fit in one block spaces. Otherwise, you would have to be a minecraft god to get through one.
The hit box and eye level are also in your feet while flying.