Hi, I am just chiming in with my results and sharing my experience installing El Capitan.
I have a MacPro 1.1 (2006). I had long updated it to 2.1. I had been running Mavericks and then Yosemite.
I used my 2011 MBP and an external drive to install El Capitan GM Candidate (I was part of the public testing so I got to download it from Apple Store). I changed the boot.efi with the same ones I had used for Yosemite while the drive was still attached to the MBP. Tried first to boot from external drive in the MacPro. Success. I moved the external drive (SSD) to the inside of the MacPro. I checked everything and it seemed fine, so I went back and installed yosefix to make sure the files don't get updated by future updates.
The computer is running really well. I did all this using a Mac Edition ATI 5770 as the installed graphics adapter. Since I read it does not support Metal, I managed to get my hands on a flashed MSI Radeon 7950. Boot screen works, Metal works, all runs great and the games run way better than before. I booted in Windows and that was success as well. The Witcher 3 looks so much better than before that it looks like a different game...
NOTE: Since installing the first non-compatible version of OSX on this Mac, I had never been able to use iMessage. It works perfectly with El Capitan, out of the box.