moteus direction configuration
Since the first public release, moteus has always calibrated motors so that a positive command is equivalent to a fixed sequencing of the phase wires. That means that depending upon which order you solder the phase wires, a positive commanded velocity will result in the motor spinning either clockwise or counterclockwise.
As it turns out, since moteus has an absolute encoder that is immune to such vagarities, it is much more convenient to normalize the direction of rotation around the encoder rather than the phase wires. As of release 2021-04-26, and moteus_tool 0.3.22, that is exactly what moteus does.