@Drexus (you may not even want my response anymore but here goes anyway)

I may not have it nailed down 100% but:
Vanilla - is when you don't have anything non Apple stock on the main installation volume, especially inside /System/Library/Extensions - iDeneb and other distro's put stuff in there by default right from square one of the install process to make OS X Leo boot from a PC (your normal Disabler, VoodooPower, BatteryManagement, fakesmc etc.) which mucks up the system for upgrade.
The concept does seem to involve keeping all that "make OS X boot from a PC" stuff separate from the main installation volume; keeping it "pure" and no different than a main installation volume taken from a real Mac. One way to get started with Vanilla is via Retail Mac OS X installation.
My take is you can create a USB installer with retail install DVD restored on it and made bootable by Netbook BootMaker - sort out issues with OSInstall.mpkg / .pkg and it'll install an OS X system that's also devoid of additives in /S/L/E.
Then finish off with EFI boot method (which is essentially just putting all those "make OS X boot from a PC" stuff in a separate place from the installation itself - a "boot layer" if you will) to make the machine capable of booting by itself.
Also, I think an /Extra folder in / works ok for this purpose - as long as you keep everything else, specially /S/L/E, untouched...