I wanted to update this headlight flickering issue to say it has been solved.
I had re-checked all the connections at the alternator, grounding points, changed the belt (was old anyway) and this was where you could still see the voltage spikes which would coincide with the flickering on the new alternator from NAPA.
Voltage display on the Torque Pro app are as follows: on the left are from the OBD and on the right is the Command Module. I'm sure they are always the same but both were avail.
I ended up ordering a new AC Delco alternator from Rock Auto and this is what solved my headlight flickering issue. Voltages are pretty much rock steady at all throttle settings.