As far as I can figure it is either intentional or an oversight of the author having originally written this with a female mc in mind, much like Choice of Romance, before changing tack and adding a gender choice.
As far as male height goes I’ve had a pretty comprehensive discussion about that with our resident tiger more then a year ago now (how time flies).
Still the mc may yet prove taller then some of the other male characters, however what irks me is that the mc is always shorter then his family members, Aeson and Saint. The heights for some of the other guys have not been established in the text yet, so it is possible that a tall mc might be a bit taller then say Santiago.
But yeah, generally the height option for male mc is currently a bit of a joke choice without any real effects.