There is a bit of magic going on in Finder with /Applications. It’s actually two folders, one in the system partition which you can’t write into and one in the data partition where anything you install goes.

There are three of them, two you've mentioned, and ~/Applications for each graphical user too.

Sadly though macOS never has and still doesn't do any magic for ~/Applications, such as showing your apps mixed in with the rest just by looking at "Applications." But yes, it does mix in the locked system apps such as Settings and Photos with the ones you have dropped into /Applications as though they're all in /Applications as they once were. I usually just add both folders to the sidebar, and forget which is which daily.