I have reviewed what has been written here regarding the Mac OS X Base System and I am still scratching my head.
The impetus for this inquiry is how these partitions interfere with booting problem resolutions. I have a 2008 Mac Pro running ML 10.8.1. These Base partitions ate not as "invisible" as one is led to believe. If I boot with the Option key to choose a boot volume, two Base partitions appear along with my primary boot partition and the Recovery partition. One problem is, when the boot drive selected in System Prefs is not "defined" in pram, the system attempts to boot from the first Base system (alphabetical?). The boot looks like booting in Verbose mode then followed by a restart only seconds after. Logs seem to indicate a Kernel Panic. Recently, due to boot difficulties, I attempted to use repair methods posted on MacFixIt.com. These methods are problematic in themselves when my system "sees" bootable volumes that aren't actually bootable!