Good news, Gareth, this is now sorted in Atlas 1.0.9.
There is a new Hide Dock icon setting in Settings, Behaviour. Switch it on and Atlas runs from the menu bar alone, staying out of your Dock and your app switcher while it carries on updating everyone's times in the background. Opening it again from the menu bar brings the main window straight back.
Atlas should automatically ask you if you'd like to update, and if not, you can open Settings and check for updates.
Thanks for taking the time to report it, it was a good catch.
Any other issues or feedback, please just get back in touch and let us know.