I have quite a few Macs that run all kinds of maintenance-(Unix-style-shell-)scripts, started up as user 'root' from launchd.
Since running Mojave 10.14 beta I see a lot of 'Operation not permitted' errors , so it seems that 'root' has lost control.
Looking at the 'problem'-files/directories from within Terminal.app I see they have permissions like: rwx-r-x---
When trying to change the rightmost permissionbits to r-x in Terminal.app (even as root) I get permission denied, while when logged in from a remote Mac using ssh I can 'chmod 755 <file>' without any problems.
Also, from remote I can rsync files/folders that carry rwxr-x--- permissionbits, but I cannot do that from within Terminal.app.