Electrons in an antenna aren't transitioning between quantum states and are still radiating.

Yes they are. They are transitioning through levels in the conduction band where you have plenty of them.

Every time you see a macroscopic phenomena, you are looking at a stupidly high amount of quantum levels with very similar energies.

That's a good point, I don't know what's up with that. Google just says, "A single oscillating electron does not continuously emit radio waves; it has a microscopic probability of emitting a single RF photon during a given cycle." It would be necessary to delve into the whole QED thing to get a better explanation, based on what I'm reading.

Either way, quarks don't have an electron-like magnetic moment, so they aren't capable of coupling to the EM field.