We've had that same setup and used the in-place upgrade approach for earlier OSes. Haven't tested it on 10.11 yet with the split partition but can vouch for it working on 10.10 and earlier.

Are you building the installer with createosxinstallpkg?

HI Yes I created a pkg from createosxinstallpkg and also I tried the downloaded os x el captan.app installer

Both have same results

@markc0

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.

I would probably test:

• Replacing the symlink in / with a Users folder
• Install the OS from the package (I'd hope this wouldn't fail as the Mac would be "normal" at that point)
• At reboot (after the install), delete the /Users folder and put the symlink back in

Yep, i have removed the symlink and placed /users back on the main partition and then ran the package
this worked fine and then re-ran my script to move the /users & create the symlink.
This worked fine, i just gotta script this now

@markc0 FWIW, we partition the Macintosh HD then use FSTAB to mount the Users partition to /Users.

That seems to still work across OS updates.

Some details here