Well, the way that the HP system works, the subsystems might not line up with the positions on the model, especially the phaser arrays, the modeled array is a very wide, but relatively thin arc or ring, while the emitter system is fairly small spherical component of the hardpoint so they will not line up exactly, there will be areas where the array model is not in the same position as the emitter.
Unfortunatly, with the D7/K'tinga, the neck is a weakness that is hard to address, you can prevent the ship from exploding outright by opening the hardpoint and setting the bridge property to non-critical, however, keep in mind the enemy will still be able to target and destroy the neck, which means you will loose any systems that are in the "head" like the sensors and torpedoes.