Assuming the box size is compensated for, there would be no difference in the sound. If the same enclosure was used for both the one mounted magnet out would have a bit better transient response but may be affected by vent noise if the motor structure is vented.
If you had two subs one mounted magnet in, and one mounted out, sharing the same volume, the method of mounting can reduce distortion compared to both woofers facing the same direction. This is the method that M & K uses in their home subs.
