This is the difference between /usr/bin and /usr/local/bin. The things managed by dpkg, rpm & co. go to /usr, and any non-packaged software should go to /usr/local (stuff built by compiling locally) or typically /opt (software supplied in binary form but not as a package). See for example the Filesystem Hierarchy Standard: https://www.pathname.com/fhs/pub/fhs-2.3.html.
The /usr/local hierarchy is for use by the system administrator when installing software locally. It needs to be safe from being overwritten when the system software is updated. It may be used for programs and data that are shareable amongst a group of hosts, but not found in /usr.
Locally installed software must be placed within /usr/local rather than /usr unless it is being installed to replace or upgrade software in /usr.
That is easily read as "non-system packages go into /usr/local", but that's obviously incorrect.
