Before or after, it doesn’t matter. Users with a reasonably up-to-date legacy launcher will get helpful errors for commands like py install (unless they genuinely have a file named install that can be launched).
It’s in the Administrative Configuration section of the docs (which is referred to, but not directly linked, from the section where you took that quote).
Chances are it isn’t going to update your existing installs anyway, since it didn’t install them. And it will be able to launch them without extra configuration if they’ve got PEP 514 registrations. Updating install_dir is unlikely to help you, and doing it using the administrative overrides is unnecessary - use a user configuration file, described in the section you were reading.
Ooh yeah, good catch, the documentation is out of date. site-packages and Scripts will be preserved for CPython installs (site-dirs is now a property in the install manifest, with the default being “what CPython used to do”).
Care to file a bug for these? The docs are still in the cpython repo, not pymanager.