Issue in disabling SIP (rootless) in El Capitan
If all functions listed are showing as being disabled, SIP is actually completely disabled; it’s just confusingly worded.

My friend had the same problem so I did some research online and found out that it is a bug. There is a bug report on this message; it is bug ID 22361698 and is cross-posted to Open Radar here:

https://openradar.appspot.com/radar?id=4932475130216448

In the above link it says to:


Boot to Recovery HD
Open Terminal
Run the following command:
/usr/bin/csrutil disable


You should then receive the following output:


System Integrity Protection status: disabled.