Because you're thinking square. Think round.
Also because you're thinking the 31% rule is for the same reason as the 40% rule.
The 40% rule is for heat dissipation, the 31% rule is to be able to fit the wires in.
For the sake of simplicity, take two wires 1" thick (nominal diameter). Now draw a circle around them. Your outside circle will have a diameter of 2".
Now take 4 wires put two on top, two on the bottom and draw a circle around them. Then draw a square around them, the corners of the squares will reach the circle. So the diagonal of the square is the diameter of the circle. Low and behold, even though we doubled the area occupied, we only increased the diameter by 40%. The circle that 2 wire occupy is 2" while the circle 4 wire occupy is only 2.8".
Now based on same assumption let's backward engineer a pipe to fill 40% with 2 wires. You'd have 0.11 between the pipe and the wire on each side (less than 1/8 of an inch), or .22 space between the wires and the pipe wall (less than a 1/4" of an inch. I'd say that is mighty hard to pull, good luck if you ever try it.
On the other hand the conduit sized for 40% fill with 4 wires will give you 0.18 from either side of the wire, or 0.36 altogether. That's almost double the space between wires and the wall of the conduit.
Like I said, you're assuming the percentage rule in both cases is for heat dissipation (or for being able to fit them in), when in fact they are for two completely different reasons.
Why is it that 2 wires are only allowed to fill a conduit to 31% whereas more than 2 are allowed til fill it to 40% of its internal area?