I assume these are a result of bad UX, at least in my personal experience.
iPhones used to/will(haven't had the pleasure in a year now) bother you quite heavily if you're at your iCloud storage cap to either upgrade or clean it out. Not a stretch that some users might not think long enough about the consequences.
Yeah I think the deleted from iCloud thing is bad UX. I don't recall the details.
The ~/Music and ~/Photos directories are basically owned by Apple though. I don't trust their apps with my files, especially when the rules change between OS versions.
