saving all files to root directory

You could certainly argue it's a bad idea from an organizational standpoint, but it is really more a question of what Apple considers good practices these days.

• Strictly speaking it's not a matter of protecting /System which has already been protected from malicious alteration for years.
• Broadly speaking Apple wants to limit potential damage to /Users and anything intended to be shared among users should be placed in /Users/Shared.

In the distant past Macs didn't care where you put anything, but as Apple's market evolved 🙄 its demographic couldn't be bothered with separating pictures from music from documents from applications. It's difficult enough to get people to understand what a "program" is, how it's not synonymous with an icon or what files or folders really represent. After all why should they be bothered with such low-level minutia. They just want their stuff to work.

For better or worse, macOS now has these predefined limitations built into it, basically to protect users from themselves.

People still manage to do questionable things though... like saving their passwords in a Microsoft Word document. Apple can only do so much.