I have just installed latest Xquartz and FSL imaging software.  I noticed that there is a new symbolic link in /usr (i.e. /usr/X11R6) to /opt/X11. My understanding was that only Apple software could be certified/signed to modify /usr under the new SIP in El Capitan.  I am certainly unable to modify /usr directly with sudo so SIP is turned on.   

Can someone explain how this works?

Thanks