tl;dr up front
Clothing are separate images that are overlayed onto the body.
Long Answer
The characters in LR2 are built piece-wise in the exact same manner that 2D artists use (i.e. The Null Hypothesis). Every body type, face type, hair, emotion, breast type, article of clothing, skin color, cum splatter, and position/stance are all rendered individually and then stitched together to create the models you see. For one position (i.e. stand 4), there are 5317 images that can be used in combination to make any given character.
As for how many images are used for a single piece of clothing? 1200. Starbuck created her own custom cop uniform for Christine, so the number I just mentioned is for the blouse piece. Clipping issues like the one from Draak are a consequence for the versatility in creating characters, scenes, and wardrobes.
To put it mildly: Vren built his own engine within Ren'Py for something he probably intended to use to create endless content.