With Yosemite and previous I'd do an update/upgrade repairing Permissions from Disk Utility before and after. It now seems like that is a edundant practice now with El Capitan... or has Repair Permissions moved somewhere?
No, your right, it's redundant. System file permissions are locked with SIP (System Integrity Protection a.k.a "rootless") active.
From the release notes for 10.11 DP: