Right now in CDVFileSystem->makeEntryForPath:isDirectory:, in the NSDictionary that is returned, for the key "nativeURL" the format is fixed (file:// protocol for a local filesystem reference, and assets-library:/ for a assets library filesystem reference.)
When calculating the nativeURL, allow this to be specified externally, check for a selector "nativeURL" and call that if available.
This is for example declared in a Category in this plugin: https://github.com/apache/cordova-plugins/blob/5d8ef21dcbde1f99d60e1b52ae3a3800e4c185d9/local-webserver/src/ios/CDVLocalFileSystem%2BNativeURL.m
... which when linked will have the selector available for the File plugin to call.
This code is part of the local webserver plugin - and it needs the File references to be proxied through a local webserver.
For example if the FileEntry is to:
.. the nativeURL would be, with this new category method, and the local webserver listening to http://localhost:8080: