fix(update_chroot): Consolidate more portage configuration

To behave more like setup_board/build_packages update_chroot should
fully configure portage to make sure everything is accurate.

Now binhosts are defined in make.conf.host_setup so the static config in
coreos-overlays doesn't need to refer to version.txt. setup_board
already made this change in 7a43a07f.

Define path locations to reduce dependency between static configs in
coreos-overlays and the behavior of the scripts repo. Spreading
configuration across two repos makes everything harder to understand.
Eventually everything should either be defined in profiles in
coreos-overlays or minimal auto-generated config files here in scripts.