99.99999999% of an atom is empty space therefore matter is 99.99999999% empty space so matter is not really as it appears and feels to our senses. The idea of using the word hologram to visualize this is a good one. It is theorized that even the particles within an atom themselves are not solid matter.
BUT, not all particles are bound by this principle. I forget which particles are free to stack up on one another in the same spot - neutrinos maybe?
I'm a bit fond of teaching my kids that the closer scientists look at matter, the more it disappears.
The mechanical range of scale of at least intellectual inquiry is mind boggling, from the Planck length (which I think is on the order of a trillionth of the "width" of a proton or something like that) to billions of light years - and as you point out, nearly all of the volume of the universe, even the so-called "solid" stuff, is empty.