Most members (including rthpjm) recommend not installing the Security Update and hiding it in the Mac App Store app. Other members have recovered by re-installing El Capitan from source, and yet more members have recovered by using a Time Machine backup, read some of the posts surrounding #3930. Forum member rthpjm has written one procedure at post #3896.

The changes made to the kernel file are believed to be unnecessary for the 1,1 and 2,1, worse, we believe that those changes are responsible for the crash/reboot loop. The Mac Pro 1,1 and 2,1 machines use Intel Xeon chip families that are NOT listed by Intel as affected by the Spectre and Meltdown issues. One of the major software components that has been modified to address these issues was the Mac OS X kernel file. The majority of this Security Update focusses on fixing the Spectre and Meltdown issues that have been widely reported. The boot process will start, almost immediately the machine will crash and restart. If you do install the 2018-001 Update you will find that your machine will go into a boot loop. Security Update 2018-001 for Mac OS X El Capitan from Apple will break your MacPro 1,1 or 2,1.

If you have OS X El Capitan up and running on your 2006/2007 Mac Pro with Pike's boot loader, you should consider disabling 'Install OS X updates' and 'Install system data files and security updates' in System Preferences > App Store so that OS X doesn't automatically install any future updates that may overwrite Pike's boot.efi. MacVidCard's guide for installing El Capitan to a 2006/2007 Mac Pro using a second El Capitan-supported Mac.rthpjm's Pikify installer script and accompanying files (and now there's an App!) can build a pre-patched OS X El Capitan installer with the Piker-Alpha bootloader for the 2006/2007 Mac Pro.

El Capitan branch of the Piker-Alpha bootloader - development thread.

Simply looking to download the Piker-Alpha macosxbootloader for El Capitan? Links: This first post has now been updated with recent summarized information.

UPDATE: Only one day later, 666sheep did it first! Who's the first to get OS X version 10.11 El Capitan booting perfectly on a 2006/2007 Mac Pro (1,1/2,1)?

Mac os x 10.11 el capitan vs sierra