If /etc/make.profile isn't correctly set, then emerging fails. Hopefully the following example make this a little more clear.
lex-jbronder / # ls -l /etc/make.profile
ls: cannot access /etc/make.profile: No such file or directory
lex-jbronder / # ls -l /tmp/pcr/etc/make.profile
lrwxrwxrwx 1 root root 70 2010-06-14 21:54 /tmp/pcr/etc/make.profile -> /tmp/portdir/profiles/default/linux/amd64/2008.0/no-multilib
lex-jbronder / # PORTAGE_CONFIGROOT=/tmp/pcr/ ROOT=/tmp/newroot PORTDIR=/tmp/portdir emerge -pv --nodeps gentoo-sources
!!! /etc/make.profile is not a symlink and will probably prevent most merges.
!!! It should point into a profile within /usr/portage/profiles/
!!! (You can safely ignore this message when syncing. It's harmless.)
!!! If you have just changed your profile configuration, you should revert
!!! back to the previous configuration. Due to your current profile being
!!! invalid, allowed actions are limited to --help, --info, --sync, and
It instantiates the config for ROOT=/ since DEPEND is installed to ROOT=/ (unless you use the --root-deps option). Even if you use the --root-deps option, it still instantiates the config for ROOT=/ in case it encounters an ebuild with EAPI 5-hdepend (this is explained in the --root-deps documentation in the emerge man page).
I suppose we could lazily instantiate the config for ROOT=/ at the point where a a DEPEND needs to be satisfied (or HDEPEND for EAPI 5-hdepend).