There’s actually a very useful package for this called Process-Palette (by morassman) that let’s you run shell commands directly from Atom. And you can run Extendscripts directly from there. Same as hitting the play button in Exendscript.
Go to Atom>Preferences and in Settings choose Install
Search for Process-Palette under Packages and click Install
Now from the menu choose Packages > Process Palette > Edit Configuration > Global Configuration
Click Add to add a new command
Give it whatever Namespace and Action Name you want.
Under Shell Command if you’re on a Mac enter:
osascript -e 'tell application "Adobe After Effects CC 2018" to activate' -e 'tell application "Adobe After Effects CC 2018" to DoScriptFile "{fileAbsPath}"'
Windows enter:
"C:\Program Files\Adobe\Adobe After Effects CC 2018\Support Files \afterfx.exe" -r {fileAbsPath}
Under Keystroke give it a hotkey that’s not used anywhere else in Atom.
Scroll down to Notifications, and you’ll probably want to turn off both Success & Error
While you’re at it another package you may want to install is: React.js (by orktes), it makes it so Atom recognizes .jsx files for the auto-color functionality.