Ah yes, no duplicate filenames does make this a bit tricky. The good news is we're planning to lift that restriction soon when the 'Flat' folder structure mode is removed. Until then I think you might have to do something a bit more hacky - perhaps you could export to Android Studio/Xcode, then add the extra files to the app. The idea is to add the extra files outside of Construct, but in a way that still bundles them with the app.