You might want to consider your deployment strategy. For example, if you need to optimize this app, both SPAs will end up in the same file. However, instead of having them both under the app folder, you can make separate folders, and give each SPA it's own main.js file.
In more advanced scenarios, you may create a "bootstrapper" app that loads one or another of the SPAs. The bootstrapper would contain code that is common to both SPAs. But each SPA (and the bootstrapper) can be optimized independently.
There are many options. Mainly, consider your final deployment strategy and that will help guide you here.
Also, the issue you have above is probably related to the fact that the standard conventions may not work in your setup, and you would need to override some functions with your own mapping.