absolutely right! there was one boot.efi on the Recovery HD and two copies inside the BaseSystem.dmg (which is stored on the Recovery HD). now in El Capitan there's still one boot.efi on the Recovery HD. but on the BaseSystem.dmg there are three copies. also, BaseSystem.dmg is the starting point to create a USB installer stick. so, I was ending up with the three efi files on the installer volume. I ran a diff on the two copies residing in /System/Library/CoreServices/ and they are identical.