We up to 10.11 have been at build time creating a separate partition and copying the /Users folder to this separate partition and then createing a sym link on the boot partition of the /Users.
This has worked well, now with the 10.11 in-place installer.
If we try to run the Os X El Capitan.app installer over the top of a 10.10.5 system that has the split disk this errors out.
I know this is down to the split disk as if i run the installer on a non split disk it works fine.
Is anyone else having these issues or is everyone installing a fresh?
Yep, seeing exactly the same thing and we are using the same split partition set as yourself. Always used Greg Neagle's tool and never had an issue til El Cap. Curiously out if the 10 or so test runs one didn't fail. I haven't tried over a single partition so it does look like it's not handling the symlink. Will pore through the log file again today so see if it yields anything useful.