It makes some sense, actually.
When the battery is full, the voltage is around 4.2V.
As the battery drains, the voltage gradually drops, probably close to 3.6V.
As Ohm’s law says: Power (W) = Current (A) x Voltage (V) , so for the same “requested” power from the battery, let’s say 10W, at 100% (4.2V) the current will be 10/4.2 = 2.38A, while at 3.26% (close to 0%), the current will be higher: 10/3.26 = 3.06A; that’s ~0.7A more - pretty noticeable difference.
More current (Amps) from the battery will generate more heat. So for the same power draw, at lower charge levels, the phone will get hotter.
You can run the Power Statistics app, select Laptop battery, History, select Rate and keep it open from 100% to 10% and compare the power draw in W (Rate) to the Charge level graph.
For battery temperature, you can use upower -d or sensors from package “lm-sensors” in Terminal. sensors will show you the current (mA/Amps) draw to (+) or from (-) the battery (only the negative values have the “-” sign prefixed), and the voltage levels.
Or just cat the files in /sys/class/power_supply/max170xx_battery/.
The better example is the other way around: when charging the battery. But keep in mind that the charge controller will push more power (and current) to the battery when it’s at lower charge levels (up to 1.7 - 1.9A from what I’ve seen) and gradually reduce the amperage as it fills up. At (close) to full, the input current to the battery is around 0.02A (trickle charging) and it should get to 0.
But the bottom line is that at low charge levels, the battery will be the hottest, due to high current (A): it gets up to 46 C on a 25C ambient temperature, that is without any significant usage load (no apps, 4G on w data off, WiFI off).
It will become a problem to charge the battery in hot environments or when you also need to use the phone heavily, i.e. the charging will temporarily stop, the red led will blink, etc.
And the fact that the Redpine WiFI module is probably the hottest component (even ~idle), doesn’t help either. I might try testing the Atheros WiFi module from the L14, for my own curiosity.
Edit: corrected minimum voltage around 0%