Unless I’m not understanding, that can’t be done from the IDE’s side (at least not completely). You’d still have to have an extension/plug-in in your text editor to hook into the IDE. (For example, my VS Code extension does the compilation part, and the story can be played directly in VS Code, mostly removing the need for the IDE.)
As for your workflow, an easy way to improve it is to write your project entirely in a project-specific extension. (Relevant section of Inform’s documentation.)
You would write
Project by wmodes begins here.
The Kitchen is a room.
[And the rest of your story.]
Project ends here.
in projectname.materials/Extensions/wmodes/Project.i7x.
Your main source file would only contain the title and include the above extension.
"My Awesome Project" by wmodes
Include Project by wmodes.
You’ll then only need to open and edit the project-specific extension in Atom, leaving the main source file to Inform’s IDE. You’ll still need to search manually mistakes in your code when compiling, but you won’t need to close and reopen your project in Inform’s IDE constantly, and the extension won’t save automatically when compiling.
This also allows to split your project into multiple files, alleviating the need to be able to jump to any heading in a single big file.