Yes, you are right on track with a battery choice decision...
With a 4171/FlexDrive build, I would install a silicon diode with the 'Hot' option to drop voltage. So you will only have one choice of batteries. 2 X CR123 primaries. You cannot use rechargeable batteries in that set up.
So with that in mind, I would recommend a 3 X AAA set up. Not only because the batteries are much cheaper, but you will have better capacity as well!
Also, you will have a choice of using normal AAA rechargeable batteries if desired.
In case you have not seen it, I have a nice side button host that looks more like the 4171 if you like that look. It uses 3 X AAA's. It's also $3 dollars cheaper... Check it out!
http://laserpointerforums.com/f39/fs-new-side-button-host-heatsink-combo-kit-22607.html