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To start the zener diodes are a normal result of manufacture in these devices. there is a typo in the description, it is Q4 that is ON not Q2. In the jag, the control causes only the high side to turn on and off while the low side completes a path for current as described. Note the three states in Fig 4-4. The on board micro interprets the pulse width modulation on the input or the CAN input and converts that to a digital value. Then it generates switching signals to control the output circuitry. There is no relation from control PWM to output PWM pulse widths or frequency. Check the schematic at the end of the document for the actual circuitry and recognize that their is a secondary power supply to generate the high gate currents used in this design. You can get more info by looking at the gate driver here...
http://www.allegromicro.com/Products...Datasheet.ashx