File Sharing in iTunes shares to whatever folder the developer enables in their app. If it is capable of supporting subfolders I’ve never seen it. Or if I have, I’ve forgoten seeing it.
But in general, since you only get access to those folder the developer chooses to share, it’s never going to be as flexible as the other apps you mentioned. Then again, it’s not as dangerous either. It won’t let you accidently change or delete a critical file.