Sharing & Permissions has two “everyone” entries, only for applications by Apple OS X 10.12.6, Sierra

My Sharing &amp; Permissions says "You have custom access" and it's showing two entries for "everyone" where the first is set to "Custom".


This only seems to be affecting every single one of Apple's applications in the Applications and Utilities folders.  I have no idea what other files are affected but a random search only turned up all Apple applications.  All third-party applications are unaffected.
I did permissions repair using Onyx but it had absolutely no affect on these applications.
I cannot manually change permissions as the minus sign is grayed out after unlocking (see picture).  Even if I could, it would take a very long time to manually find/repair.
I do not know what triggered this problem as I just discovered it today.  However, I recently cloned my hard drive over to a new solid state drive using Carbon Copy Cloner.
I've already followed this official Apple procedure for fixing my Home folder permissions and I don't seem to have any problems there.
Everything appears to be operating, however, I'm seeing some strange problems like my ICC color profile will not stick after a reboot (permissions seem fine in the Library), but the ColorSync Utility instantly crashes when I click the "Repair" or "Verify" button.




I've already found and followed this thread, but the answer did not help.
This is a normal behavior of the Sharing &amp; Permissions Info window in macOS systems protected by SIP.

The three latter are the POSIX permissions:

rwxr-xr-x@  3 root      wheel  restricted   102 Jul 22  2017 Activity Monitor.app
    com.apple.rootless

rwx read/write(/traverse(execute)) for the user root/system
   r-x read(/traverse(execute)) for the group wheel
      r-x read(/traverse(execute)) for everyone


The first entry (everyone > Custom) is a result of the restricted flag/com.apple.rootless attribute and can be interpreted as an ACL: group:everyone deny delete and the ACL can't be modified!



An (older) list of all restricted/SIP protected files and folder can be found here: System Integrity Protection – Adding another layer to Apple’s security model