Ah I see, I knew of the periscopic part of the gunner sight but couldn’t understand the reason for the increased recess.The gunner sights are periscopic, meaning the gunner sits considerably lower in the turret so that he's securely behind the frontal turret armor. The commander requires greater situational awareness, so his sight sits higher (and rotates) to allow an unobstructed 360-degree view.
The reason gunner sights are recessed in a 'cutout' on Type-99A is probably because the height of the turrets is considerably greater than that of Type-99, that and increased top protection makes the gunner sight appears more recessed.
As for the other turrets you mentioned, the same applies; so long the gunner sits behind the frontal armor, he's ok.
Thanks for the info, really appreciate it.