FreeBSD's default .profile has a hardcoded PATH and other platforms (e.g. Mac OS X) likely have it as well: http://svnweb.freebsd.org/base/releng/9.1/share/skel/dot.profile?view=markup It is probably a good idea to include a note in the "Gentoo Prefix Bootstrap Process" document about this. It would be even better if bootstrap-prefix.sh did a test for it at the end of the bootstrap process so that it could display a warning to the user.
it did (does)
See bootstrap_startscript in bootstrap-prefix.sh, it should check if PATH is kept/respected.