app-portage/gentoolkit has the dependency to portage defined as DEPEND="sys-apps/portage" This can lead to a situation where gentoolkit is installed for PYTHON_TARGETS which aren't enabled on sys-apps/portage. The dependency should read DEPEND="sys-apps/portage[${PYTHON_USEDEP}]"
~/gentoo/gentoo $ grep sys-apps/portage app-portage/gentoolkit/*ebuild app-portage/gentoolkit/gentoolkit-0.5.0-r3.ebuild: sys-apps/portage[${PYTHON_USEDEP}]" app-portage/gentoolkit/gentoolkit-0.5.1-r1.ebuild: sys-apps/portage[${PYTHON_USEDEP}]" app-portage/gentoolkit/gentoolkit-9999.ebuild: sys-apps/portage[${PYTHON_USEDEP}]"