Right. The PS2/3V charging circuit is about 5V. So the supercap will charge up to about 5V. The battery "chemistry" limits the charged 2-cell battery voltage to about 2.4V.
Peeling the layer of the onion - this might make you cry. The reason you want to charge the supercap to ~5V is because energy stored is proportional to the square of the voltage. So the same supercap charged to ~5V has 4 times the energy vs. if only charged to 2.4V. The PS2/3V battery circuit is smart enough to process the higher supercap voltage as well as the lower battery voltage.