I have deployed my Node JS app onto Google Cloud App Engine, and I can successfully add my custom domain for my app.
Let say my custom domain is example.com
You can do it just using the dispatch.yaml file from App Engine, list all your domains there, but not the *.appspot.com one. Google will show a 404 route when you try to access that.
dispatch.yaml
*.appspot.com
EDIT: Not possible anymore, check comments.
Checkout the official reference.