Actually, it goes to my point that Carbon, Hydrogen, and Oxygen atoms are uniquely different, as we might also say of the Father, Son, and Holy Spirit. Yet each atom is made from the same subatomic particles (same in substance) and together they form a molecule with unique properties. Ooooh, this analogy just keeps gettin' better. My intent is not to reduce God to "wood and stone", as it were, but to demonstrate that there are observable, graspable concepts which help us to see that the idea of a Trinity or a Godhead is not completely unfathomable. As an analogy, I like it better than any I have heard to date. But, as with all analogies, it is not a comprehensive description, only a means of helping us to better understand certain concepts.
You point out the problem of carrying an analogy too far. I agree that you get substances with different properties and behavior if you start changing the number and orientation of the O, C, and H. So, yes, my illustration is open to criticism, but I think that within the limits of the scope of its application, it is a useful one.
Now I kinda wish I had taken more chemistry back in the day. It's really a fascinating subject in itself.