After checking with our engineers, they tested that this current firmware on the engine board did successfully output PPS. As 1PPS is a very small pulse (1uS) to be measured; thus, 0V is always indicated even with a 3D fix.
Without good oscilloscope and equipment, a user may miss the PPS output. That's why it's happening as you have stated. Since our firmware and hardware have confirmed that it supports PPS output, they suggested to adjust the oscilloscope.
Furthermore, they added that integrating Zener Diodes for protection would not help because 1uS pulse is too small. Also, it happens instantly. For that reason, you see that the voltage is always low.