The problem is that each run step gets its own shell instance, so the export doesn’t carry over. To set an environment variable for the rest of the job you need to use the set-env workflow command:

- run: echo "::set-env name=CR_PAT::GITHUB_CONTAINER_REGISTRY_PAT"

After that either of the references should work. Or, if you need CR_PAT only in that one step you could use an env property for the step:

- run: echo ${CR_PAT}
  env:
    CR_PAT: GITHUB_CONTAINER_REGISTRY_PAT