"I took it as "Not Connected", but wanted to be absolutely sure"
I'm glad you checked and verified. I run into this all the time when it comes to IC pin designations. I err on the side of caution and assume the prohibitive meaning unless the datasheet expressly indicates the "pin not connected" definition. The error in writing a manual is in assuming a familiar convention translates elsewhere and carry the same interpretation.
Your original question was regards to "parking" unused unipolar (6-wire) motor wires; please leave them unterminated and insulated at the motor end. While I'm at it, I'd like to just mention a few other things may have already taken care off:
1) If you run a 6-wire motor in the 'half-winding' mode, set the current to the motor's rated current. If you run the motor in 'full-winding' mode, set the current to 1/2 the motor's rating.
2) Use 18-gage wire for the motor cable. Any wire-gage substantially less than that will cause the cable to overheat. Do not use manufactured connector and cable sets marked 'serial port cables'. They are intended for milli-amp loads like mice and use 28 gage wire.
3) Use the mating DB-9 connectors we supply with the G540. DB-9s come in 1 Amp and 5 Amp per pin flavors and you can't tell the difference by looking at them. The 1 Amp ones will overheat (3.5A being pushed thru a 1A pin) and damage the mating G540 DB-9 connectors.
4) Place the current set resistor on the G540 end DB-9 cable connector. Putting it at the motor end results in noisy motors because the motor wires in the cable inject noise into the current set connections.
5) Do not use a power 'On/Off' switch the DC side from your power supply. Put the 'On/Off' power switch on the AC side going into your power supply.
6) Have the power supply near (1ft or 300mm) the G540. If it must be further away, Place a 2,200uF to 4,700uF capacitor rated at 63VDC across the G540 power input terminals. Mind the capacitor's +/- voltage polarity.