atom_plugin_less_settings_1.js

// ...
const { writeFile } = require("fs");
const { join } = require("path");

module.exports = {
  // ...
  activate() {
    atom.config.observe("packagename.SettingName", updateStylesheet);
    return this.subscriptions = new CompositeDisposable();
  }
  // ...
};

function updateStylesheet(value) {
  writeFile(join(__dirname, "..", "styles", "custom.less"), `// AUTOGENERATED\n@SettingName: ${value};\n`, "utf8");
}