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?
Repair Permissions
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:
"Disk Utility
Note
System file permissions are automatically protected, and updated during Software Updates. The Repair Permissions function is no longer necessary."
https://developer.apple.com/library/prerelease/mac/releasenotes/General/rn-osx-10.11/index.html