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.
I agree. I imagine I am a character in a game and God is the gamer playing the game. OP just asked, if God is made of pixels. Imagine this weird question...