electron-builder: Problems with native modules

My workflow for an electron app is

# Install all dependencies, including native modules
npm install

# Ensure native modules are built to match electron
./node_modules/.bin/electron-rebuild

# Test the app
./node_modules/.bin/electron .

# package the app
./node_modules/.bin/electron-packager . \"MyApp\" --out=dist/osx --platform=darwin --arch=x64 --version=0.33.6  --icon=assets/osx/myicon.icn

# build a distribution
./node_modules/.bin/electron-builder \"dist/osx/MyApp-darwin-x64/MyApp.app\" --platform=osx --out=\"dist/osx\" --config=packager.json"

The last step is failing with the following error:

- Starting build for ´osx´ - 
Writing temporary ´appdmg.json´
Wrote temporary ´appdmg.json´
Kicking off ´appdmg´
module.js:355
  Module._extensions[extension](this, filename);
                               ^
Error: Module version mismatch. Expected 14, got 46.
    at Error (native)
    at Module.load (module.js:355:32)
    at Function.Module._load (module.js:310:12)
    at Module.require (module.js:365:17)
    at require (module.js:384:17)
    at Object.<anonymous> (/Users/xxx/projects/myapp/myapp/electron/node_modules/electron-builder/node_modules/appdmg/node_modules/ds-store/node_modules/macos-alias/lib/create.js:7:13)
    at Module._compile (module.js:460:26)
    at Object.Module._extensions..js (module.js:478:10)
    at Module.load (module.js:355:32)
    at Function.Module._load (module.js:310:12)

I believe this is happening because the electron-builder script is running using a node implementation incompatible with electron (which is why the electron-rebuild script is necessary):

$ npm --version
2.5.1
$ node --version
v0.12.0
$ ./node_modules/.bin/electron --version
v0.33.6

Is this a bug? What is the recommended way to build build distributions with native modules?