The metadata/layout.conf file can be considered as an essential part of the profiles, since it can affect their interpretation via settings such as profile-formats. Therefore, it makes sense to sync this file when the profiles are synced. This change will make --sync-submodule=profiles more useful for binhost clients, since it syncs the minimal amount of the tree necessary to have a working binhost client.
There's a patch in the following branch: https://github.com/zmedico/portage/tree/bug_559122 I've posted it for review here: https://archives.gentoo.org/gentoo-portage-dev/message/9766ac2181607740c9ef637bcc05f2af
This is in the master branch: https://gitweb.gentoo.org/proj/portage.git/commit/?id=4a3f6ce8e5c64b7447bb32851ee91e19faf18be3
Released in portage-2.2.21