Sure, 3xRCR123A in your M3T will work fine. The limitation is that the smaller RCR123A cells typically have a capacity (C) of about 500mAh and the max recommended current draw from a standard Li-Co Li-ion is 2C (about 1A). This is right around the current draw if you want to drive an MC-E at full power (e.g., 1.4A for a 2S2P MC-E) using 3xLi-ion. If this is an issue, an alternative would be use the Li-Mn based IMR16340 cells, which can be driven at 8C. I am fairly conservative and don't run my MC-E towers at full power. Full power means a lot of heat. See
this post. Since your M3T uses the KT4 TH, I would avoid full power to an MC-E tower.
Run time using the LED is much longer than with the incan. In an old SF 12ZM, run time with 4x123A and the stock N62 lamp is around 10 min with decreasing lumens with time. I can get over an hour for one of my MC-E towers with essentially constant output.
Hot spot lux is typically better with the incan lamps, at least initially. Remember, the incans steadily decrease in output vs time. An SSC P4 tower runs a close second in hot spot lux. The bigger die MC-E is known to be a floodier emitter for the same reflector. Still, the MC-E still has good throw.
Unfortunately, making a good apples-apples incan vs LED comparison using a KT4 is hard. My host is a SureFire M900 3x123A sized weaponlight. I don't have a KT4 incan lamp that can run using 3x16340 Li-ions. This is the data I do have:
KT4, 2S2P K-bin MC-E, SOB1000 driver, 3xAW16340, 6500 lux at 1 meter
KT4, 2S2P K-bin MC-E, SOB1227 driver, 3xAW16340, 6700 lux at 1 meter
KT4, SSC P4 U2SWOH-bin, SOB1000 driver, 3xAW16340, 9100 lux at 1 meter
Z46, MN11, 3x123A, 7800 lux at 1 meter
Z46, MN11, 2xIMR16340 (SF E2 host), 11000 lux at 1 meter
Even though the MC-E towers don't have the peak lux of the others, the MC-E hot spot is very large, the spill is bright, and the overall light output is high. And the MC-E hot spot lux is still comparable to my Malkoff M30 (and about 3X of my old Blackhawk Gladius), so it's no slouch. The P4 hot spot, in contrast, is smaller. That's why the P4's peak lux is much higher -- its beam is focused down to a smaller point.