I think the answer is in the link you provided.
My guess is that system relies on this assets to be present in all .apk files. But instead of building them in (which would increase size of all .apk files), Android emulates them via asset API.
I think @Taifun can tell you if its extension makes these system folders invisible.
If these folders are physically in assets, I also think the file component is behaving correctly. Whether we want these folders to be visible or not is another question.