Apple has stated that the "rootless=0" boot argument to disable System Integrity Protection is temporary and will be gone in the GM version of El Capitan. Allowing this route to disable the feature would defeat the entire purpose of it.
Source? They said in the WWDC session (http://asciiwwdc.com/2015/sessions/706) that the process to disable rootless may change during the beta, but didn't say that it won't be possible in the GM.
They know that rootless will break some applications/drivers, plus some types of development may need it disabled.
