No, but you can quickly tell what is a part of the base system vs not based on where it is located. Your /usr directory typically isn't empty on a new Linux install, whereas /usr/local is totally empty.

A simple example is if you run 'which vim'. If you have installed vim through pkg on FreeBSD it will show up in /usr/local/bin/vim. Whereas if you run 'which vim' on Ubuntu, it will show up in /usr/bin/vim -- but on Ubuntu Desktop (when I last used it) vim is preinstalled. You can't just look at the /usr directory on a Linux machine in most cases and know what was installed when you installed the machine.

From viewpoint of organizing backups separating system stuff from host specific makes some sense. Also, you can put /usr/local on separate volume, this allows mounting rootfs read-only which can be useful in some cases.