If you read my guide with due attention, you'll notice that all such operations are supposed to be carried out using the Terminal on the INSTALLER partition, not the live El Capitan partition. If you run all the relevant commands from the installer, you'll be root by default, and you'll be able to bypass whatever SIP configuration you may have on your El Capitan partition(s). Please, note that changing SIP settings or using sudo is unnecessary. The Terminal of the installer has EVERYTHING you might deem necessary.
Yup. Success!
I was able to update the Recovery HD when I was booted off another disk.
Thank you team!
- David