And here we go, my new blog article is out:
"Atom plugin "gitlab-integration" leaks your tokens"
https://shivering-isles.com/Atom-plugin-gitlab-integration-leaks-your-tokens
TL;DR: When you use the Atom plugin gitlab-integration you should either patch it with the mentioned workaround in the article or stop using it. Definitely you should revoke the personal access token you were using with it.