Dan,
There are many ways to setup your machine for this process.
A US Digital MA3 shaft encoder for analog or PWM laser modulation timing belted to the Z axis stepper would allow the Z axis down movement and laser modulation at the same time, but they would be synchronized together. A variable feedrate can be used also.
Or, you can use a switch for different stepper motors. Set the Z axis focal height, then switch to the MA3 stepper to control the laser modulation with Z axis commands. A variable feedrate can be used also.
Or, you can use a DAC or a MA3 as a 4th axis. Z axis down movement commands & A,B or C axis laser modulation commands can be set independently, but still on the same line of gcode. You can also vary the feedrate.
There are other options and somewhat similar, but they are out of Mach3's ability. It consists of using X, Y axis moves and then S commands for the laser's modulation. A variable feedrate can be used with it also.
You can try just using a variable feedrate, but by using both variable laser power and variable feedrate combined together, it gives you more control of the outcome as you can see in my examples.
Jeff