Yes the LiFePo4 has a smaller capacity (rated at 500mah) than the regular Li-ions. 500mah may sound little compared to a primary, but then again, it all depends on your usage. The P1D Q5 consumes approx 350ma in primary mode, 1100ma in turbo and 40mah in low mode on a freshly charged battery at about 3.31 volts. it consumes a little more current when the voltage drops. Assuming that primary mode is used most of the time, that should translate to about 1 hour of total usage theoritcally. FrenchyLED did a runtime and it was somewhere between 50min to just over 1 hour: see post #116 at
http://www.cpfmarketplace.com/mp/showthread.php?t=125353&page=4
I came across somewhere else (maybe do a search) where someone else did a runtime with regular protected 3.0V Li-ions and I believe the runtimes were roughly similar to the LiFEPo4. The runtimes I believe are longer with the 3.7 volt li-ions but then you'll lose your primary and low modes. Runtimes with Primaries are the best, but stick with brand names. Then again, the regular Li-ions and Lithium primaries (especially cheap ones) run the risk of venting - as this forum has shown. Granted, the risks are very small - but they have happened, even with single cell flashlights.
The LiFEP04 cells work for me and my P1D Q5 because of the way I use it. First of all, I use the P1D as an EDC. It is always stored in my coin pocket in my jeans and I use it typically for about 5 -10 minutes (on primary/low modes) a day. These cells are not supposed to be drained too low as they do not have a protective circuit. To prevent over dischage, I simply swapped a freshly charged battery every week or so regardless of what's left in the cell. I would also change it more often if intended to be used for lengthy periods of time. I also carry a spare charged LiFePo4 cell in my bag/car in case of emergencies. I have a set of 4 LiFePo4 that I rotate. So far, this setup works perfect for me. Best of all, I do not have to worry about venting issues! I think the minor inconvenience is worth the peace of mind.