Enterprise Territory Management now supports the ExternalID type of custom field on the Territory2 object. This means you can create a custom field that appears on territory records and use that field to store external IDs. Query and report on that field within Salesforce.
For details on creating custom fields, see “Create Custom Fields” and “Custom Field Attributes” in the Salesforce Help. Make sure to add your custom field to Territory record page layouts, and let your team know how to use it.