Don't assume this is run from the chroot and point explicity to it.

src/scripts/enable_localaccount.sh

 #!/bin/bash
 # Copyright (c) 2010 The Chromium OS Authors. All rights reserved.
 # Use of this source code is governed by a BSD-style license that can be
 # found in the LICENSE file.
 set -e
 
 if [ -z $1 ]
 then
-  echo "Usage: $0 localaccount_username"
+  echo "Usage: $0 localaccount_username [chroot_path]"
   exit 1
 fi
 
+# Default chroot_path to its standard location
+chroot_path=${2:-"../../chroot"}
+
 echo "Enabling local account $1@gmail.com."
 echo "Remove these files to disable:"
 
 for namespace in pam_google pam_offline
 do
    file=../platform/$namespace/pam_localaccount.h
    [ "$namespace" = pam_google ] && namespace=chromeos_pam
 
    echo $file
 
    cat <<EOF > $file
 // local username for Chrome OS pam
 // This file is auto-generated by enable_localaccount.sh
 
 #ifndef CHROMEOS_PAM_LOCALACCOUNT_H_
 #define CHROMEOS_PAM_LOCALACCOUNT_H_
 
 namespace $namespace {
 const char kLocalAccount[] = "$1@gmail.com";
 }
 
 #endif // CHROMEOS_PAM_LOCALACCOUNT_H_
 EOF
 done
 
 # Add CHROMEOS_LOCAL_ACCOUNT var to /etc/make.conf.user
+echo "Setting CHROMEOS_LOCAL_ACCOUNT in $chroot_path/etc/make.conf.user..."
 VAR_NAME=CHROMEOS_LOCAL_ACCOUNT
-if grep -q ${VAR_NAME} /etc/make.conf.user; then
+if grep -q ${VAR_NAME} $chroot_path/etc/make.conf.user; then
    regex="s/${VAR_NAME}=.*/${VAR_NAME}=$1@gmail.com/"
-   sudo sed -i -e "${regex}"  /etc/make.conf.user
+   sudo sed -i -e "${regex}"  $chroot_path/etc/make.conf.user
 else
-   sudo sh -c "echo ""${VAR_NAME}=$1@gmail.com"" >> /etc/make.conf.user"
+   sudo sh -c "echo ""${VAR_NAME}=$1@gmail.com"" >> \
+               $chroot_path/etc/make.conf.user"
 fi