I never used the ~/Documents folder. Lots of apps just trashed their stuff in there over the years making that folder entirely unusable for my actual document files. I would have to dig through the mess to find them. So I have to admit that I don't really understand the extra "care" Apple is doing to this particular folder. Same for the ~/Downloads folder: all my actual downloads go to some other disk, since the system disk is so small. Protecting this two folders would be entirely useless here.

IMHO where it really needs to be protected from when iCloud suddenly starts grabbing everything w/o the user's permission to upload it to some random Apple servers.