The current version needs the files to be installed inside <internal or sdcard>\Android\data\bruenor.magicbox or otherwise you won’t be able to get MDB see your files.
You might want to send an email to the admin as he can give you a beta version of MDB which works around Google’s storage restriction.
edit:
Be careful with uninstallation. If ever you put your game files inside the Android folder of your device, make sure to move them elsewhere before uninstalling MDB (if you plan to). This is because uninstalling MDB will also delete the bruenor.magicbox folder which has your game files.