>>11109962OP here, you're mostly right. The thing is why I go for 3 is not because I haven't thought things through, quite the contrary. It's from my decade of experience working with applied QM in solid state and molecular systems. When you really get down to the nitty-gritty and try to figure out ions and electrons fit together to make matter, and try to predict measurable properties from that, you start to realize that there are no electrons whizzing about. You have ions held together by a static smear of charge density, and that charge density is made up of "electron".
Within that charge density you can either ionize a free electron or excite a quasi-electron that carries charge, but at no point would you have anything that could be considered "empty space". (Unless you're talking about nanoporous materials, but that's something else.)
The people claiming atoms are mostly empty space are only thinking of one specific case, namely measuring the position of an electron to figure out where it is, or something like Rutherford's gold foil experiment. Indeed, the electron position will collapse to something tiny -if you force it to-. But that's not how atoms and molecules interact with each other in the real world.
On Rutherford's experiment, people tend to draw the completely wrong conclusion from it. The conclusion is not that the atom is mostly empty because most electrons move through unimpeded, the conclusion is that nearly all the mass of the atom is condensed in a nucleus that is far smaller than the atomic scale. It's like throwing a tennis ball around a hallway and saying the hallway is empty because the tennis ball is moving through unimpeded. But trying to use that knowledge of the "empty hallway" to try to talk about air currents or weather patterns makes zero sense.
