You’re way over thinking this. You’re also grossly overestimating how large an atoms is. They are so tiny and do in fact undergo bonding and electron exchange which means molecules will stay together. It’s not like you could simply move mass through the atoms of a molecule. Atoms strongly interact and there are such a large, unfathomable number of atoms in every object that the effects of atoms being mostly empty space are negligible. You need to think in terms of how the real world actually works and not how it should work based on 1 piece of information about quantum physics.
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