We know far less about matter, because our very selves appear to us to be made, not of matter, but of mental stuff. A universe that was filled with mind, or a universe that was designed by a mind like ours, would be far less mysterious than the one we inhabit. There is nothing more mysterious than matter itself, its raw existence and presence. Consider the photon. It is never emitted or recorded except as a particle, yet in between it often behaves as a wave.
Physicists can write out the maths of quantum physics.
We don't need to plumb the deep of quantum physics to see the mystery of matter. Consider the background image from the Hubble Space Telescope, a furnace of star creation in the galaxy M33. It resembles for all the world the illuminated clouds with which baroque painters used to surround images of Gods and angels. Come down again to earth. Hold a pebble in your hand and feel its solidity.