No, they wouldn’t.
They would exist outside of our universe (since they created the universe), so the rules of physics in our universe don’t apply to them.
Even if the reality they existed in had something equivalent to atoms, it would be inaccurate to call those “atoms” since they are in different realities.
It only applies if he took an oath to uphold the constitution prior to committing the treason.
I.E. government officials and ex military personnel who took place in the Jan 6 riots would be disqualified, but not every random yahoo that was there.
EDIT: Others have pointed out that he is ex-military, so it looks like the 14th amendment does apply to him after all.