Add portage to [global] in /bedrock/etc/bedrock.conf:
etc = adjtime, crypttab, default/grub, fstab, group, group+, group-, group.OLD, group.org, gshadow, gshadow+, gshadow-, gshadow.OLD, gshadow.org, hostname, hosts, login.defs, machine-id, modprobe.d/blacklist.conf, passwd, passwd+, passwd-, passwd.OLD, passwd.org, rc.local, resolv.conf, resolvconf/run, shadow, shadow+, shadow-, shadow.OLD, shadow.org, sudoers, portage
Then
sudo brl apply