Well, I kept digging and ultimately found a very long running issue thread[1] that mentioned having a .git directory in your home directory can cause high CPU.
Removing the three year old and accidentally created ~/.git directory and restarting Atom fixed the problem.
So now I will give Atom a deep new look.
Still, I am a bit perplexed, this is an issue that has been reported for nearly two years, and has not been fixed. I am not sure about the technical nature of the problem, but I think Atom, is trying to digest my entire 340GB home directory. Assuming that this is desired behavior, there should be at least a warning at launch about the issue. I am sure that MANY people have accidental ~/.git folders, and have a bad experience with Atom. At the vary least, it should not have taken me a couple hours of digging to find a solution buried in a GitHub issue.
While this fixes the issue on my MacBook, I am not sure about the Mac Mini, which I don't think will have a .git directory, but I will check later tonight.
[1] https://github.com/atom/atom/issues/3426#issuecomment-119780...