Why do I need to deploy a "default" app before I can deploy multiple services in GAE?

The reason is that there are also several app-level configs, applicable to all services/modules:

• dispatch.yaml
• index.yaml
• queue.yaml
• cron.yaml

Some of these configs can have trouble if not deployed after/together with the default service. And some services may have dependencies on the app-level configs.

The requirement of deploying default first is simply a measure to reduce the risk of initial deployment problems. Subsequent deployments no longer have this restriction (since default is already deployed)

Yes, the default service is mandatory (sort of like a kitchen sink for all kinds of stuff, for example requests not matching any dispatch rule are sent to the default service). So just declare one of your non-web apps the default one (it doesn't matter what the default service actually does).

Somehow related (mostly for the examples): Can a default service/module in a Google App Engine app be a sibling of a non-default one in terms of folder structure?