I am not familiar with the term "low side driver".
However, these outputs are the multi-function pins, set in GUIDE to PWM, for either setting amps, or a duty cycle. (pinconfig 3 and 6, I beleive)
If there is no way to do this is software, I'll set up, like you, a series of relays to cut signal power.
However, this needs to be addressed in the next iteration of hardware produced by SDF.
Having outputs go to anything but ZERO upon power-up, or power-off is completely unacceptable.
No other piece of machinery or hardware controller that I've used is designed this way.
It's unsafe, it's uncontrolled, and most importantly, it forces you to add extra hardware electronics when it should be covered by the microcontrollers being built properly.