The models express the positions of the nuclei of the component atoms and the bonding connections. Yest atoms do really take on the shape of something like the models but only "something like". Atoms are not spherical balls. Bonds are not sticks nor stick shaped.
So yes a "VSEPR model is a tool to help us visualize what is happening to molecules". They cannot represent the quantum nature of the electrons surrounding the nuclei nor how their behavior dictates the types and strengths of the bonding between atoms nor effects of excitations and such.