I can only speak for myself but I'm pretty sure I expressed an understanding of your post by indicating I do something similar in Windows 10. (SIMILAR, I said, but not identical to your request.)
What I will ask is what your problem is? So what if there's an 'active desktop' folder that you choose to not use. You still get what you want, right? An empty desktop that doesn't interrupt your wallpaper?
I don't like the concept of a Downloads folder (since I prefer my Desktop) but I wouldn't ask Windows or Ubuntu to move or remove said folder. Just don't use it.
I'm too new to Ubuntu to know if there's a way to make Desktop a hidden folder.