Raspberry PI 3 - LiFePO4 power supply
...6.4VDC is closer to Vout (5VDC) so it will be a more efficient power supply than Vin as 9.6VDC.

That is true if you would be using a linear regulator since then the current remains constant. But then the 3 cell solution would give a longer battery life as the individual cells can drop to a lower voltage until the regulator cannot provide 5 V anymore.

But you should use a switched regulator since that is going to be much more efficient for the currents needed by an RPi. And for a switched regulator efficiency will be better when the input voltage is higher.

The most efficient solution is 3 cells and a switched regulator.

I suggest not to make your own switched regulator as that might end with all kinds of issues. There are cheap ready-made switched converter modules for sale which will just work saving you a lot of trouble. My suggestion: find an LM2596 based module, these are cheap as chips and will just work. These can also supply up to 3 A or so, more than enough for an RPi.