I'm just going to ramble a bit here, so bear with me, and hopefully some of what I have to say will make sense and/or be helpful with understanding this whole PWM issue...
I'm not aware that there's a temporal difference in persistence between rods and cones, but I'd have to look it up to be sure. I'm not an expert on rhodopsin characteristics, but one of my professors from grad school when I was getting my PhD in perceptual psychology at UC Santa Cruz, Gene Switkes, is... I'll have to look up some of his papers and see if he's done anything on differences in the characteristics of the pigments in rods vs cones. Just of the top of my head, I'd say that sensitivity to PWM because of differences between rods and cones is more about the differential sensitivity they have; a cone requires 5 - 6 photons to generate an action potential, whereas a rod only requires 1 - 2, so your hypothesis is certainly possible, but I'd think that overall even with the PWM the total light output would be enough to activate the cones, and at that point the intensity of the light is so high the rods get overwhelmed and essentially shut down and don't work (as in photopic vision).
With respect to flicker sensitivity, the critical flicker fusion (CFF) rate is a function of the intensity of the light. The greater the intensity of the light, the higher the rate needs to be for the light to be perceived as continuous rather than strobing/flickering, so in general, a lower PWM rate is less noticeable at low levels than high levels. I'm not an electrical engineer, so I don't know if it's possible to design a circuit that would vary the PWM rate based on the output level, but I would imagine it's cheaper and easier to build a driver that uses the same rate at all output levels. Still, the reason as to why the 2C uses such a low rate is baffling to me, and aside from the fact I don't do 123 format lights, I'd never get one because I am fairly sensitive to PWM.
Anyway, please pardon the early Sunday morning ramblings of a tired old psychophysics professor... haven't had my caffeine yet...
PS: I have to say, I really like the beam profiles of these lights... I love the large hotspot in the beam... the idea of having most of the beam be hotspot and the minority of it as spill is a very appealing profile to me for my EDC preferences. Although I find the poor regulation a put-off and the fact they're only available in cool tints right now too means I'll be waiting until they come out with neutral versions (IF they come out with neutral versions that is...)