FWIW: WinClone does work fine if you first boot into "Recovery" mode and disable SIP in terminal, then reboot and do your WinClone changes, then reboot and re-enable SIP. This isn't necessary when simply saving an image of your Windows environment, you only need do it when modifying or creating a new Windows installation from your WinClone image.
It is too bad that you can't simply run the Yosemite version of Disk Utility under El Capitan to regain the lost features and ease of use especially in regards to partitioning and RAID. Have to refresh my Terminal Unix memory and do it that way I guess. (Although, I too keep a Yosemite install SSD handy in my Mac Pro.)