"You said your name was Harmon, right?"
There was something particular about Atlas' alias. He only learned after he entered the Tower, but it seemed that the Divine Being he was named after was alive in this ecosystem. His name was practically blasphemy. It was only considered differently because of his circumstances.
He found himself facing those circumstances when he had to find an alias to use consistently.
There wasn't a problem when mortals did it. They didn't know any better. Atlas' name was given to him by his parents, so no God could question its veracity.
However, the situation would be different if he personally chose to steal a God's name for an alias. That level of disrespect would not be tolerated.
Atlas didn't know much about the Gods, but he knew that they were entities he could not offend at his current level. Therefore, he chose to use the name of someone he used to know instead.