I can't reproduce that on MBPr running 10.11.1.
Note that after disabling SIP in Recovery Mode and then booting normally, csrutil status will report:
System Integrity Protection status: enabled (Custom Configuration).
Configuration:
Apple Internal: disabled
Kext Signing: disabled
Filesystem Protections: disabled
Debugging Restrictions: disabled
DTrace Restrictions: disabled
NVRAM Protections: disabled
This is an unsupported configuration, likely to break in the future and leave your machine in an unknown state.
So it says "enabled (Custom Configuration)" but all it's component parts are disabled and so it is effectivly (and in practice) disabled.
-Max