How does CS determine the size/position of the red/green/blue placement box around items?

And is there a way to override that calculation or set the size/position within a nif file?

I ask because there are items that the placement box does not exactly match the model.

For example: Furn_De_R_Bookshelf_02 - there is a small gap between the bottom of the placement box, and the bottom of the bookshelf.

That is the collision box. It can only be altered in a 3D rendering program, like Blender or NifSkope.