In principle, it makes no difference: the HV laser power supply will accept either analog or PWM signals. It has an internal low-pass filter to demodulate the PWM into the analog control signal it uses to set the tube current.
However, the controller generates its analog output by filtering its PWM signal, so feeding that to the power supply means it gets filtered twice and has a lower bandwidth.
This might begin to matter when engraving dithered photographs at high speed, where the laser must reach full power and turn off within the span of a single pixel. The double-filtered bandwidth smooths the sides of what should be a crisp pulse and reduces its maximum power.
In round numbers, the shortest good-looking pulse you can get will be on the order of 3 ms. Scanning at 400 mm/s means that dot will be 1 mm wide, which corresponds to an image resolution of only 25 dpi. That we all get decent results at ten or twenty times higher resolution with similar speeds suggests the numbers aren’t everything. 
Bottom line: use the PWM output.
Far more than you probably want to know about bandwidth on my blog:
The linkies there refer to all the measurements & background info.