Should this sentence "With all the motors hooked up, you can connect the 12v power." be read as "DO NOT connect the 12v power if you don't have all the motors hooked up" ?
If so, it might be worth insisting a bit :)
I think the issue is that the A4983s can be damaged if the motors are connected or disconnected while power is applied. Applying power with no motor connected is ok, just don't connect the motor until it's off!
Technically, connecting the motors shouldn't damage anything, but getting a quick, clean connection with physical connectors is nigh impossible and contact bounce will lead to momentary disconnection and the spikes which damage the chip.
Time will tell if the robustified A4988 is better protected in this regard.