2. In a few encounters it was described by Allied pilots that the Me-163’s would leave contrails at times when their engine was on, and then at times they would cut it off for a bit before cutting it back on. I know the Komet had a throttle, but could the pilots turn the engine on and off during flight without any trouble?

I’d highly doubt that they had time or fuel to restart those rocket motors.
The contrails may have been either T or C Stoff Leaking off after the other ran out? Just a thought