Since v0.11 Atom IDE UI has a terminal and it seems to be possible to open it with a given command: facebookarchive/atom-ide-ui#220 (comment).
It would be nice to have a command to open sbt shell inside Atom. It could be also useful to suggest it (as a notification with a button) when launching Metals, if there is no running sbt server yet (project/target/active.json).