Hello michiganstud,
If your ultimate goal is runtime, your best bet is going to be to run a single larger Li-Ion cell to drive the module, this will reduce your output some, but will give you a very efficient use of the cell through the discharge, with a steady but barely noticeable drop in output through the discharge.
The stock 6P does not have room for an 18650 (you could run a single 17670 if you want), but if runtime and recharge-ability in that platform are the goal, then you'll want to pick up an 18650 compatible body for the light. CPF member Nite is selling some FM brand bodies that are really decent over in the custom-mod/BST section of this forum.
As far as rechargeable vs primary runtime comparisons, this is a comparison that is not really fair to make, but I will try to summarize some of the important points:
A pair of CR123s packs slightly more stored energy than a single 18650 cell when the 2 configurations are compared at a LOW drain rate (like an LED module).
A single 18650 packs slightly more stored energy than a pair of CR123s when the 2 configurations are compared at a higher drain rate (like an incandescent module).
A Single 18650, with its lower voltage than a pair of CR123s, will operate most buck regulated LED modules at a lower (read "direct drive or less") output than would be the case on a pair of CR123s. This results in less output, but much more runtime because less energy gets used over time.
So... the answer to most of your questions will always depend on the specific configurations being compared.
If your main goal is to get really good runtime, then I suggest you take the following things under consideration:
1. RCR123s are the worst option for maximizing your stored energy.
2. Something with multiple modes will allow you to run for extended periods of time with less power consumption.
3. Just because a pair of CR123s technically has more stored energy than an 18650 at low drain rates, does not mean that you will always be leaving the house with a fresh set of CR123s loaded. With Li-Ion cells, you can "top off" your cells whenever you feel like it. This means that you are always starting "fresh" and never have to play the guessing game of how much of the batteries you have used up and whether you need to bring along spares.
-Eric