I have configured my git editor both by:
git config --global core.editor \"atom --wait\"
or
git config --global core.edito
I don't have atom installed, but I did a similar thing for VS Code. Have you tried putting the command and the switch together inside quotes?
editor = 'atom -w'
I've been doing that with the Bash EDITOR
shell variable, since my default editor changes depending which OS I'm on at the time, whether I'm using SSH or not; so setting it inside the Git config for a project is not a solution for me. But it may be for you.
So please try that and tell us what happens.