Is there a benefit to charging a supercapacitor in parallel and then discharging in series?
With a given hand-crank X and super capacitor Y, if you stack up several Y's to charge with X, this will be lighter work, but will take longer.
That last part is of course simply conservation of energy.

If crank X cannot supply the stacked voltage, you will not get them full and parallel would be an option.

Your initial conclusion is correct, you get a higher visible capacitance and lower resistance, but to a generator/crank this is actually "more work".
Think of a low resistance as a short circuit and a high resistance as unconnected wires. Try to turn the crank with nothing connected, then short the crank and try to turn it again.

You will soon find the short circuit is a lot more work.

Edit, due to your comment above:

Be aware that the K-Tor, as advertised, supplies 120VDC. No 12V at all. You will need a switching power supply to be able to transfer the 120VDC somewhat efficiently to a 12V bank of power buffers such as the caps you want to use. In which case you are free to optimise for the capacitor bank you build. (13V5 for 5caps stacked, for example).