That's working as intended to improve loading times and performance (and maybe to stop the breasts from clipping through the top because you'd have two separate pairs with simulated physics, this may actually be the main reason why it exists). It's usually the breasts when having the top equipped, but if I remember correctly, it could also be the hips when you're wearing pants. A quick way to see if your piece of clothing has these issues is to export the texture, make it fully transparent and then import it again in the character creator.
Disabling this setting most likely requires you to fiddle with the game's core code. But I'm not certain of this.