So we are mostly electron clouds... and clouds by definition are mostly empty space.
At the scales our brains are familiar with we experience "emptiness" as a kind of space which can have things placed in it. A chair is empty if you can sit on it, a box is empty if you can put something in it. The sub-atomic "empty" space is filled with fields of various kinds. You could not place something where those fields are. The spaces are not empty.
When you fill a box with things, you are filling it with sub-atomic fields.
Shoot a neutral particle through that cloud and you generally find it really was empty. Wave particle duality doesn’t mean a particle is in every location, just that it could be in every location. After detection you generally find all the places it was not.
And wave particle duality could mean that a particle is a wave when it's not being detected.
> Inside your body, you aren’t mostly empty space. You’re mostly a series of electron clouds, all bound together by the quantum rules that govern the entire Universe.
> So we are mostly electron clouds... and clouds by definition are mostly empty space.
But empty space isn't .. er .. empty ...
My point is that one cannot settle this sort of issue by invoking the definition of words. I am not sure what sort of fallacy the 'argument by dictionary definition' is, but it is definitely a fallacy (except possibly in lexicography.)
> look, you're not just empty space > just kidding! yeah you are
Atoms are mostly "empty space" in the same way that the gap between a maglev train and its track is empty space (ignoring the air).
Atoms are fuzzy things without a hard interface boundary. At that scale it doesn't really make sense to say they have a "perimeter" at all. The distance at which they repel each other is different from the distance at which they cling together in a hydrogen bond, which is different from the distance between covalently bonded atoms, etc. The electrons themselves roam all over the place, including far outside whatever bond distance you might choose as the size of an atom. In short, there isn't a perimeter which defines "inside" and "outside" of the atom.
The "empty space" thing is a bit of a poor analogy anyway. It comes from chemical experiments which showed that the repulsive cross section of an atom when pummeled with zero-charge particles is orders of magnitude smaller than the electric cross section. These are different forces though (strong vs electromagnetic), so it's a bit apples-to-oranges to begin with.