I can't give a well referenced answer to the OP, but my strong guess is that you would want to ground the neutral of the wye for the same reason that you would want to ground the neutral of the wye secondary of a typical drive isolation transformer. 1) You want to stabilize the voltage to ground of the secondary and the voltage to ground of the DC bus to help protect the motor insulation system and 2) you want to provide a path for switching noise currents that are capacitively coupled to ground through the motor frame. The reason that this is a guess rather than a solid answer is that I'm not sure what happens to the delta secondary voltage to ground.
To answer post #2:
In a bridge rectifier (of any number of phases) you only have one pair of diodes conducting at a time. The most positive phase gets coupled to the + DC bus, and the most negative phase gets coupled to the - DC bus.
In a normal 3 phase rectifier, each phase is most positive (or most negative) for 120° of the AC cycle. Each specific pair of diodes conducts for 60°, so you have 6 conduction 'pulses' per AC cycle.
The 12 pulse transformer gives you more secondary phases, so the conducting periods for a specific diode pair gets reduced and the number of pulses per cycle gets increased. With multiple separate secondaries you might also get overlapping conducting periods, but again that is outside of my work.
The net result is lower DC bus ripple and lower harmonics reflected to the transformer primary.