After spending more time than I would like to admit trying to figure out why I couldn't see any El Cap 10.11 related updates in the NetBoot/SUS branches I finally figured it out.
We are running the NetBoot/SUS 4.0 Appliance on a Linux VM.
I found there was a typo in the following plist on the NetBoot/SUS. Path /var/lib/reposado/preferences.plist
See attached images for how the plist did read and how it now reads.
After the fix to the plist is made just run the following to sync the SUS.
$ sudo python /var/lib/reposado/repo_sync