Mind to check that you are using latest master??

If not, tell me which branch are you using to test it.

Working for me (latest master), I ran these steps:

cd
mkdir firstboot
cat > firstboot/one_two.yaml << EOF
heat_template_version: 2014-10-16

resources:
  userdata:
    type: OS::Heat::MultipartMime
    properties:
      parts:
      - config: {get_resource: one_config}
      - config: {get_resource: two_config}

  one_config:
    type: OS::Heat::SoftwareConfig
    properties:
      config: |
        #!/bin/bash
        echo "one" > /tmp/one

  two_config:
    type: OS::Heat::SoftwareConfig
    properties:
      config: |
        #!/bin/bash
        echo "two" > /tmp/two

outputs:
  OS::stack_id:
    value: {get_resource: userdata}
EOF

cd
cat > firstboot/userdata_env.yaml << EOF
resource_registry:
    OS::TripleO::NodeUserData: one_two.yaml
EOF


#Deploy the overcloud as:

openstack overcloud deploy \
 --libvirt-type qemu \
 --ntp-server pool.ntp.org \
 --templates /home/stack/tripleo-heat-templates \
 -e /home/stack/firstboot/userdata_env.yaml


### Also with your example:

cd
cat > firstboot/first_boot_update_hook.yaml << EOF
heat_template_version: 2014-10-16

resources:
  userdata:
    type: OS::Heat::MultipartMime
    properties:
      parts:
      - config: {get_resource: update}

  update:
    type: OS::Heat::SoftwareConfig
    properties:
      config: |
        #!/bin/bash
        yum update -y

outputs:
  OS::stack_id:
    value: {get_resource: userdata}
EOF

cd
cat > firstboot/first_boot_env.yaml << EOF
resource_registry:
    OS::TripleO::NodeUserData: first_boot_update_hook.yaml
EOF


#Deploy the overcloud as:

openstack overcloud deploy \
 --libvirt-type qemu \
 --ntp-server pool.ntp.org \
 --templates /home/stack/tripleo-heat-templates \
 -e /home/stack/firstboot/first_boot_env.yaml



#Both examples working and running in latest master.

Some logs..

[stack@instack ~]$ heat stack-list
WARNING (shell) "heat stack-list" is deprecated, please use "openstack stack list" instead
+----+------------+--------------+---------------+--------------+
| id | stack_name | stack_status | creation_time | updated_time |
+----+------------+--------------+---------------+--------------+
+----+------------+--------------+---------------+--------------+
[stack@instack ~]$ openstack overcloud deploy \
>  --libvirt-type qemu \
>  --ntp-server pool.ntp.org \
>  --templates /home/stack/tripleo-heat-templates \
>  -e /home/stack/firstboot/first_boot_env.yaml
Removing the current plan files
Uploading new plan files
Started Mistral Workflow tripleo.plan_management.v1.update_deployment_plan. Execution ID: 1a3863f4-38c2-40b1-ada5-cf7292ca2a76
Plan updated
Deploying templates in the directory /tmp/tripleoclient-QYqpWY/tripleo-heat-templates
Started Mistral Workflow tripleo.deployment.v1.deploy_plan. Execution ID: b62e6757-a79f-4ef1-8b86-c2ae7d030cc6
2016-11-24 11:03:28Z [overcloud]: CREATE_IN_PROGRESS  Stack CREATE started
2016-11-24 11:03:28Z [overcloud.MysqlRootPassword]: CREATE_IN_PROGRESS  state changed
2016-11-24 11:03:28Z [overcloud.PcsdPassword]: CREATE_IN_PROGRESS  state changed
2016-11-24 11:03:28Z [overcloud.RabbitCookie]: CREATE_IN_PROGRESS  state changed
.
.
.