the qrc approach is the last step when publishing a game and not the ideal workflow during development. The main advantage you get by using the qrc approach, is that you can protect your QML source code.
So you might test performance in release builds and still not use the qrc approach. Or not use qrc in release builds because especially when not using shadow builds the workflow is much faster (because you can just perform a re-run of the appliation without compiling it).
The third reason why we decided against the autamitc switching as you suggested is this: When you add a new folder in your project tree, you manually need to add this folder to the resources file. As your app would not start if you forget this step, this is a manual process you usually do when your app is ready for publishing and thus the better user experience is to use the DEPLOYMENTFOLDERS approach during development.