So the strong force holds the protons (& neurtrons) together, and then the charge of the protons must balance the charge of the electrons in terms of the electromagnetic forces. I think my main problem was with the whole idea of gluons acting on protons and neutrons but not electrons, and photons (EM) acting on protons and electrons but not neutrons. So it seems there could not be a primordial-type of atom - Hydrogen must be the start element. I still feel there's something I'm missing. Probably a good book on the subject