As far as I am aware no controllers change the voltage that limits laser power. There was talk of using a digital to analog converter on the retinaengrave but I don't know if that has happened yet.
Your statement is correct:
"...the plugin cycles the laser depending on how dark the particular pixel is, which is what I imagine the software is doing when it's duty-cycling as well."
Currently controllers just use PWM (
http://en.wikipedia.org/wiki/Pulse-width_modulation ) on the TTL line. There are virtually no advantages to controlling the voltage - As you have discovered the voltage to laser power relationship is non-linear and would possibly change with temperature.
The only place where analog control of the laser would have an advantage is if you are moving faster than the frequency of the PWM (or switching time of the laser).
Any requirement to play with the potentimeter is mainly a limitation of your controller. Both the retina and DSP allow engrave and vector cut power to be adjusted so the potentiometer is redundant (useful only for very very low power since switching time can make 0.1-1% slightly more powerful than intended).