Unfortunately, this is why I left Atom and went to VS Code. There was a terminal package, and it was great. (github.com/jeremyramin/terminal-plus/issues) But, then they applied a gamechanging "upgrade", and it basically forced all packages to be updated as well. The result being abandonment, on many popular ones.
There were a few forks, but they all had the same issues of not working well cross-platform. Cursors disappearing/appearing in the wrong locations, console not loading, etc.
The last one I used was platformio-atom-terminal, which I could no longer find on Github.
Go with VS Code. It's much better, imo - and I'm a hard guy to convice when it comes to switching add-on toolsets.
VS Code extensions seem much more reliable, and the editor itself is impressive.