This currently happens in the EncodedMotor class - is there a real reason to move it into the encoder instead?
From my perspective the flipping is necessary when the positive orientation of the encoded motor doesn't match the positive orientation of the robot. I don't think the Encoder class is really being utilized outside of the primary case, but I can see the argument to change it as long as the EncodedMotor class is additionally updated to match this change.

Not all encodered motors use the same direction convention. I bought some N20 motors where the convention was flipped for example. From what I remember, flipping the motor direction is no help because that also flips the encoder direction. They will always be opposite. Unless you can flip the encoder direction separately.