Not really an issue ATP, as the turret "fits in the hole."
Docking shuttles, etc, inside is an abstraction, but one that I can live with.
Bay weapons as turrets is canonical. Bays as pullable modules ("cans") is also canonical. And the two are not incompatible. Think of the extra tonnage as the needed track and traverse gear.![]()
The volume of the turret outside the bay is no more than 10%, based upon AHL and GT. So you get maybe 10 tons outside the bay.
Movable Mounts: If the weapon is enclosed it is called a turret. A larger turret (over 600 kiloliters*) is called a bay.