It would make a lot of sense for all non system files to go in /USR & system files it /root. Sorry this might seem lie a stupid question, but it make sense ifyou ask me.
Next time use a search engine of your choice first 
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And why makes it sense to put system files in the home folder of the root user?
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Ok /boot makes sense & /usr is the old /home, so ok /bin & /sbin make sense Also /tmp, but it could have all the from the old days folders removed right?
You also should read
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Why do I have 10 fingers?
It has turned out over time that this is the most flexible solution. According to the current state of the art, it doesn’t get any better if you take the given requirements into account. (This is the view of many experts)
https://www.jw.org/en/library/bible/nwt/books/genesis/1/#v1001027
https://www.jw.org/en/library/bible/nwt/books/genesis/1/#v1001031
It is similar with the linux Filesystem Hierarchy Standard. It has proven itself.
What difference does it really make to the average dumb bell user like me. It’s not like I have to access those files more than a couple of times a year. You really want to see a confusing file system, check out the Windows! How many “My Documents” do I really need to see? Do they still use that insane Registry? God what a mess of logic.
Sorry, didn’t mean to offend. Agree 200% about the horor of the regesty, good idea, MS just let monkeys actually arrange it.
No offense taken. But as mentioned by others, if you have general questions about Linux the search engine will be your friend.