I'm not fully versed in how the EFI booting process happens. If I want to install Linux in a partition formerly used by Windows, why can I not simply use LILO, installing the boot section in the "root" instead the MBR? Thanks.
The BIOS emulation only kicks in if you use MBR or hybrid GUID + MBR partitioning. By default, Macs only use GUID partitioning. Installing Windows via Boot Camp enables this hybrid partitioning, but you can in principle also do it manually for Linux. The downside is that you then have to maintain two partition tables and make sure to keep them in sync.
It is rumoured that you can still boot Mac OS X from a pure MBR, too. I've never tried this, and even if it does work, I suspect things like firmware updates and FileVault 2 FDE will not work in such a configuration. You'll probably also have problems with multi-booting unless your bootloader supports OSX directly.