having the system mounted in its own sub directory rather than be spread over multiple directories (there's /usr/bin, /usr/share, /usr/lib, etc) has the advantage that a single read-only mount can mount the whole OS.

Having the OS mounted read-only provides some security benefits.

The other option would of course be to have / mounted ro and then have rw mounts in /home, /etc, /var and /tmp, but this is more complicated than a a rw / and a ro /usr