Should I interpret that you actually used "my" build of Pike's boot.efi, El Capitan edition, and that you can confirm it works? Please, explain further.
It's the first build of Pike's new branch (for El Capitan) of his macosxbootloader. I know it involves SIP compatibility, but I don't know to what extent or what exactly that entails.
I've seen your dialogue with Pike in his Universum site. I interpret that "my" build of boot.efi, El Capitan edition, is good enough to boot El Capitan with SIP fully enabled, but possibly not good enough to run the OS X installer, i.e., the recovery environment. Perhaps you can report on the refinements Pike has advised as to whether you finally succeed in booting your El Capitan recovery partition on the old Mac Pro.
Hmmm. Would the regular Yosemite version of Pike's boot.efi boot the latest recovery partition of El Capitan for you? My guess is it wouldn't. We'd better ask Pike. Perhaps the "final" version of Pike's boot.efi, El Capitan edition, will do what you want. As you know, it's still partially crippled, as it can't read from NVRAM, which probably means it's more restrictive than it should.
The presence of that second boot.efi inside BaseSystem.dmg was already detected in the Yosemite Recovery HD. One of the forum users discovered that if it was replaced with Pike's Yosemite version, Option booting of the Recovery HD was still possible à-la-Mavericks and previous versions, in addition to the new Command-R, customary from Yosemite onwards.
I'm quite certain that what I reported was reasonably accurate, but I can't find the post. I think it's in the thread "2006/2007 Mac Pro (1,1/2,1) and OS X Yosemite". Please, notice that I didn't mention a file named "bootbase.efi". As I recall, whoever the discoverer of Option-booting the Yosemite Recovery HD was, he didn't mention a different name: just a hidden copy of boot.efi within the dmg contained in the Recovery HD. If that dmg wasn't altered, Option-booting didn't work (it would probably boot Yosemite itself, not the Recovery HD). However, if it was altered placing Pike's boot.efi inside, Option-booting was again a possibility. Cmd-R-booting, however, could still work without modifying the dmg, provided the regular boot.efi of the Recovery HD was replaced with Pike's version.
The Yosemite Recovery HD contains, among other things, ONE boot.efi and at least one (possibly two) inside the dmg it uses to install the system. I never modified that dmg in my Recovery HD, which meant I couldn't Option-boot with it (it would simply boot Yosemite itself, not the Recovery HD), but if the boot.efi in uses for Cmd-R booting was replaced, that would boot the Recovery HD on an old Mac Pro. I can't be more specific because I no longer have a Yosemite Recovery HD. My HD got a lot of bad sectors, so I transferred Yosemite to an SSHD with no Recovery HD.
