This is expected.
Files packaged in the applicationDirectory are compressed as part of the APK and don't have a direct file system path. You will need to extract them to an accessible location, (applicationStorageDirectory).
In AIR simply copy the File reference to the File.applicationStorageDirectory and then you should have a native path reference if you really need that.
var file:File = File.applicationDirectory.resolvePath("includes/audio/bird.mp3");
var fileAccessible:File = File.applicationStorageDirectory.resolvePath("bird.mp3");
file.copyTo( fileAccessible );
trace( fileAccessible.nativePath );