Comment by topspin

> it should be possible to completely forego the pulsebased approach and only drive the motors using regular (and less frequent in comparison to pulses) position instructions

Since that capability is present, it's probably worth your while to apply it. Good motion control is hard, but important. Unnecessary vibration due to phase noise in the pulse train is an example of the subtleties that matter at high frequency. Excessive force generated when moving large masses can prematurely wear drive components and, over time, backlash increases and you get precision and repeatability problems. Well managed motion control will mitigate these things.