Let's not forget the whole partition split situation due to the 1024 cylinder limitation. Once upon a time, you couldn't get to certain parts of the disk from your bootloader (using BIOS calls), so you had to make something like a tiny /boot which would hide < 1024.
This situation has only improved a little. There are still lingering bits of it here and there, depending on how deeply you poke and which distribution you have installed.
People who are serious about having an encrypted system should have absolutely none of the bootstrap process residing unencrypted on the disks of that system because somebody could take out the drive, look through the boot process, and log your passphrase.
I have an encrypted laptop that boots from a read-only USB key that is attached to my keyring. It will only boot from this keyring (and a backup CD-R that I have), and the system and the boot media are never stored together. Before USB keyrings became common, I would have the boot media be a CD-R.
These limits are chiefly imposed by the BIOS (int 10h) calls available to a boot sector program (the 512 bytes of machine code you get inside the master boot record of a disk), and require a lot of cleverness to escape from.
This situation has only improved a little. There are still lingering bits of it here and there, depending on how deeply you poke and which distribution you have installed.