We are not really talking about the player's height here though. It's more of the eyes height above a seated point (torso and neck height), which can also be very different from person to person and would affect how scale is perceived. Mind you, it's easy to adjust to once you are aware of the difference but it can take people by surprise and lead some to assume that the scale is wrong from their perspectives.
The issue is not only eye height above seat but floor height of ship vs reality. The seat is very high in the ships, hence ship floor will not match reality. Your brain will scale down world as it knows where floor really is. Bar stools have been suggested