I'll try to clarify.... You are absolutely correct that LEGO drops their sets into the boxes vertically, but the flaps are always on the top and bottom. This way the flutes (those little wavy pieces in the middle) always stay vertical. You get the most edge crush strength when the flutes are vertical. The way you've stacked your packing boxes, all of the flutes are horizontal which means the LEGO boxes inside are carrying a fair bit of the load from the second and third rows.
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