The overlay has now release4.1 branch. A new template will be built with correct overlay branch selected. In order to prevent any next R4.2 possible compatibility breakage like with qrexec or gui-agent, for user already having Gentoo installed please do:
$ echo "sync-git-clone-extra-opts = --branch release4.1" >> /etc/portage/repos.conf/qubes.conf
and remove the existing git repository located at /var/db/repos/qubes in order to force emerge to clone the appropriate branch.