Settings for atom are now stored in the gist at https://gist.github.com/RealOrangeOne/9f9a4dd799ad01aa0502a09f06cbf454/ and synced using this plugin.
This makes syncing them between machines far easier than my old implementation of Owncloud sync and symlinks!
Unfortunately, this setup also stores the version number of the plugins, which means that a revision has to be made every time a package needs to be updated. It does kindof annoy me with all the spam, but at least it's not really obvious, and I'm sure there's a way of cleaning it up!