Hate to pitch a total crackpot theory, but WSM (Wave Structure of Matter) would postulate that the funky shape of those bounds has to do with the enclosed regions between them, the blue (or red) bubbles outlined by the bonds. In WSM theory, covalent bonds are formed by "shade cones," fields of force radiating from atomic nuclei like little tractor beams that have the ability to capture electrons. The path of those cones can actually be deformed by regions of higher energy density (the colored regions) since in WSM, it's the incoming energy of radiation pressure that forms those force fields in the first place.