Basically if your addon does not call SetRuntimeModuleMainScript(), it creates a default one that imports all runtime scripts - in this case including myModule.js, which isn't how you want imports to work. When you call SetRuntimeModuleMainScript(), then Construct only imports main.js, and then all other scripts are loaded by imports - which allows you to choose not to import every runtime script, and instead set up a tree of imports.
When the next stable update is out I'll update all the SDK samples to use SetRuntimeModuleMainScript() so you can use those as templates.