if I remember correctly, Steve said that he hardcoded so that android can only boot from external memory. However, things could have changed.
You can change the partition from which you want to boot in system chooser. Example from multiboot config:

ITEM_NAME="Debian"
ITEM_ID="debian"
ITEM_DEVICE="${EXT_CARD}p1" # you can change EXT_CARD to INT_CARD and put the correct partition number instead of "1"
ITEM_MODULES="mbcache jbd ext3"
ITEM_FSTYPE="ext3"
ITEM_FSOPTIONS="noatime,rw"