It seems strange to me that Atom is experiencing the same sort of troubles that occur with large multi-project projects and they don't seem to be aware that their tooling should accommodate that.
One thing that is blatantly obvious would be a organization wide issue tracker. That alone would alleviate the "which project do I file this against" questions and give the project owners an easy way to see the issues for all of their projects.
I work on a few projects that are actually multi-org, so even that wouldn't be enough for me, but would be a darn good start.