Based on your comments, you are using Github Repo as the repo resource. In this case, you need to set the Repo Resource to reference the Github repo.

I am afraid that the Repo Resource doesn’t support using the variables to define the branch in checkout step(e.g. - checkout: repo@$(prjref)).

We need to define the define ref settings in Repo resource to define the checkout branch.

For example:

resources:
  repositories:
  - repository: MyGitHubRepo
    type: github
    endpoint: MyGitHubServiceConnection
    name: MyGitHubOrgOrUser/MyGitHubRepo
    ref: ${{ variables['Build.SourceBranch'] }}

steps:
- checkout: MyGitHubRepo

The ref field in Repo resource only supports compile time variable (e.g. ${{ variables['Build.SourceBranch'] }}).

Refer to this doc: resources.repositories.repository definition

ref name to checkout; defaults to ‘refs/heads/main’. The branch checked out by default whenever the resource trigger fires. Template expressions are supported.

Currently, Azure DevOps only supports using runtime variables in Inline syntax checkout. But only Azure Repos Git repositories in the same organization can use the inline syntax.

For more detailed info, you can refer to this doc: Check out multiple repositories in your pipeline

Update:

For a workaround, we can spilt the single pipeline into two pipelines to run the two stages. One is used to set the variable and pass the value to parameters in Pipeline two. The other Pipeline use the parameters collect the branch name and use it in the ref field.

Here is an example:

Pipeline One

stages:

- stage: build
  jobs:
  - job: config
    steps:
    - checkout: self
      clean: true
      submodules: recursive
      persistCredentials: true
    - task: CmdLine@1
      inputs:
        filename: Call
        arguments: (here calling a script which sets PRJ_BRANCH, removed for Export Control)
    - task: PublishBuildArtifacts@1
      inputs:
        PathtoPublish: '$(OUTPUTDIR)'
        ArtifactName: Reports
      condition: succeededOrFailed()
    - task: PowerShell@2
      inputs:
        targetType: 'inline'
        script: |
              $token = "$(pat)"      
              $url="https://dev.azure.com/{Orgname}/{Projectname}/_apis/pipelines/{PipelineRunID}/runs?api-version=5.1-preview"
              
              $token = [System.Convert]::ToBase64String([System.Text.Encoding]::ASCII.GetBytes(":$($token)"))
              
              $JSON = "
              {
                
              
              
                `"resources`": {
                  `"repositories`": {
                    `"self`": {
                      `"ref`": `"refs/heads/main`"
                    }
                  }
                },
                `"templateParameters`": {
                  `"Outputref`":`"$(PRJ_BRANCH)`"
                },
              
              
              
              }"
              
              
              $response = Invoke-RestMethod -Uri $url -Headers @{Authorization = "Basic $token"} -Method Post -Body $JSON -ContentType application/json  

Pipeline Two:

parameters:
  - name: Outputref
    type: string
resources:
  repositories:
  - repository: repo
    type: github
    endpoint: MyGitHubServiceConnection
    name: MyGitHubOrgOrUser/MyGitHubRepo
    ref: ${{ parameters.Outputref }}


stages:

- stage: projectconfig
  jobs:
  - job: test
    steps:
    - script: echo ${{ parameters.Outputref }}
    - checkout: self
      # clean: true
      # submodules: recursive
      # persistCredentials: true
    - checkout: repo  

In this case, the variable value: PRJ_BRANCH will be passed from Pipeline one to Pipeline two -> parameters. And it can be used in the ref field of the repo resources.