The workflow I have deployed/enabled globally is a SharePoint 2013 workflow.
SharePoint 2013 workflows are hosted on the Workflow Manager platform.

To add the workflow on all Libraries, we need to add a new workflow subscription to the workflow manager using the ID of our Workflow definition.

To find the workflow definition ID:

$Web = Get-SPWeb http://site/web/ #Web where the Workflow feature is enabled.
$wfm = New-object Microsoft.SharePoint.WorkflowServices.WorkflowServicesManager($web)
$defSevice = $wfm.GetWorkflowDeploymentService()
$wfDefs = $defSevice.EnumerateDefinitions($false) 
$wfDefs | Format-Table ID, DisplayName

Set the workflow definition ID from the above result into the $WorkflowDefinition variable below.

$Web = Get-SPWeb http://intranet/web/ 
$Web.webs | ForEach-Object {
  $_.webs | ForEach-Object { #I'm targeting 3rd Web down.
    $wfm = New-object Microsoft.SharePoint.WorkflowServices.WorkflowServicesManager($_)
    $defSevice = $wfm.GetWorkflowDeploymentService()
    $wfDefs = $defSevice.EnumerateDefinitions($false) 
    ### Update below variable with yours
    $WorkflowDefinition = "Workflow Definition ID goes here"
    ###
    $wfDef = $wfDefs | where {$_.Id -eq $WorkflowDefinition}

    $wfTaskList = $_.Lists["Workflow Tasks"]; #Task and History lists must exist, see note below.
    $wfHistoryList = $_.Lists["Workflow History"]

    $_.lists | where { $_.BaseTemplate -eq "DocumentLibrary" } | ForEach-Object {
      if($_.title -eq "Site Assets")
      {
        write-host "Skiping Site Assets"
      }
      else
      {
        $wfSubService = $wfm.GetWorkflowSubscriptionService()
        
        #Create Workflow Subscription 
        $sub = New-object Microsoft.SharePoint.WorkflowServices.WorkflowSubscription
        $sub.DefinitionId = $WorkflowDefinition
        $sub.Enabled = $true
        $sub.Name = $wfDef.DisplayName

        #Build start options
        $startOptions = New-Object "System.Collections.ObjectModel.Collection[System.String]"
        # $startOptions.Add("ItemAdded") #When item added
        # $startOptions.Add("ItemUpdated") #When item updated
        $startOptions.Add("WorkflowStart") #Allow manual start
        $sub.EventTypes = $startOptions

        $sub.SetProperty("HistoryListId", $wfHistoryList.Id)
        $sub.SetProperty("TaskListId", $wfTaskList.Id)
       
        try{
          $wfSubService.PublishSubscriptionForList($sub, $_.Id);
          write-host "Workflow" $wfDef.DisplayName "successfully associated to" $_.title
        }
        catch{
          write-host "Workflow FAILED to associate for" $_.title
        }
      } #End Else 
    } #End Lists Loop
  } #End $_.webs Loop
} #End $Web.webs Loop

The task/history lists must exist in each library before running the above code.
Enabling the Publishing feature on a site creates these for you. You can do this through PowerShell here. (refer to bottom of post)

Resources:
– StackExchange question answered by Caroline which is where I got the basis of the above code from.
– Great post on Get-SPScripts which shows adding a workflow through PowerShell and seems to add the Tasks/History list if they don’t exist.