I installed the 10.11.1 update while still in Target Disk Mode to my Mac Pro from my Macbook Pro (while booted to my Mac Pro's drive). you do this via a Firewire cable from your Mac Pro to your Macbook Pro, then reboot your Mac Pro while holding "T" on the keyboard until you see a Firewire logo... the Macbook Pro will now see the Mac Pro's drive(s) as if it is a giant hard drive enclosure, allowing you to install OS X to the drive(s) or boot via the drive(s) without removing them from your Mac Pro... I tried using a USB enclosure, but it kept failing on the first install reboot. Target Disk Mode worked 100% the first try (and Firewire 800 is faster than USB anyway).
I did all of my updates that way immediately after upgrading my Mac Pro's drive to El Cap. Then I just booted the Macbook Pro to its native drive (which is also running El Cap, but not 100% necessary) and did the following while the Mac Pro was still in Target Disk Mode:
first you need to be able to have all files visible on your Macbook Pro. mine already was, but in case you're wondering... in terminal:
defaults write com.apple.Finder AppleShowAllFiles YES
then re-launch Finder (alt+click finder in dock, relaunch)
open finder to the Mac Pro's drive
the first boot.efi is at: /System/Library/CoreServices/boot.efi
run this command to unlock it:
sudo chflags nouchg [drag and drop the boot.efi to terminal to get the exact path]
copy and paste Pike's boot.efi to the CoreServices folder on your Mac Pro drive, then re-lock the file (I've been told this isn't necessary, but whatever) in terminal:
sudo chflags uchg [same path]
next boot.efi is at: /usr/standalone/i386/boot.efi
this one you can just replace (it's already unlocked) -- copy and paste Pike's boot.efi to this folder, replace existing boot.efi
after I did this, I ejected the Mac Pro drive from my Macbook Pro, disconnected the Firewire cable, and rebooted the Mac Pro. it booted right up on first try.