Author of `linter` / `linter-ui-default` here. The package in no place in its code rewrites the entire Atom package configuration. It does however observe it's own configuration. If observing in itself resets the Atom config, then it's out of the hands of the package and a bug in Atom core.

It's possible that one of the linter providers had that issue, and since Linter providers are only called by the linter package, they wouldn't exhibit the issue on their own. It's not uncommon to have issues that seem like it's the linter's fault since all of the providers do nothing and seem harmless unless invoked by the linter package.

I would've helped to debug this, had somebody pinged me on any of the issues. Oh well :)