The article from the source states that the electrode tips are 2 cm apart. That is actually sufficient information to determine how much larger the dot is than the actual atom.
“The article from the source states that the electrode tips are 2 cm apart.”
2 cm is ~ 3/4 of an inch so the dot is millions of times larger than a single atom. IMO seeing the glow from a single atom is not the same as seeing the atom itself. Besides, how do we know the dot is from one atom and not a cluster of many?