I may be waaaaayyyy off base here, but I had always considered /usr as a receptacle for things that aren't part of the base OS.
As there are /bin and /sbin, there are /usr/bin and /usr/sbin. These are for third party additions of binaries or scripts.
Likewise, /usr/local/bin and usr/local/sbin for things the user creates for themselves.
Third part application bundles though, should go in /Applications for all users, or /Users/username/Applications (not a thing, by default, and the applications have to be able to handle that location, too).
What reeeeeeealy bugs me is the undefined status of what is an Application, and what is a Utility.