There is a bit of confusion about what is the _source datum and the created fields with the formula transformation.
I've cleaned up it a bit and now it looks fine at least on the vega editor online.
I've also slightly changed the way you get the Region as it looks like not always available in the labels object but can be part of the OrgHier object.
{
  "$schema": "https://vega.github.io/schema/vega/v5.json",
  "description": "An example of Cartesian layouts for a node-link diagram of hierarchical data.",
  "width": 1000,
  "height": 800,
  "padding": 5,
  "signals": [
    {"name": "labels", "value": true, "bind": {"input": "checkbox"}},
    {
      "name": "layout",
      "value": "tidy",
      "bind": {"input": "radio", "options": ["tidy", "cluster"]}
    },
    {
      "name": "links",
      "value": "diagonal",
      "bind": {
        "input": "select",
        "options": ["line", "curve", "diagonal", "orthogonal"]
      }
    },
    {"name": "separation", "value": false, "bind": {"input": "checkbox"}}
  ],
  "data": [
    {
      "name": "table",
      "format": {"property": "hits.hits"},
      "transform": [
        {
          "type": "formula",
          "as": "OrgId",
          "expr": "datum._source['labels.OrgId']"
        },
        {
          "type": "formula",
          "as": "Region",
          "expr": "datum._source['labels.Region'] || datum._source.OrgHier.Region"
        },
        {
          "type": "formula",
          "as": "StoreNum",
          "expr": "datum._source['labels.StoreNum']"
        },
        {
          "type": "formula",
          "as": "RegisterNum",
          "expr": "datum._source['labels.RegisterNum']"
        },
        {
          "type": "fold",
          "fields": ["OrgId", "Region", "StoreNum", "RegisterNum"]
        }
      ],
      "values": {
        "took": 11,
        "timed_out": false,
        "_shards": {"total": 23, "successful": 23, "skipped": 21, "failed": 0},
        "hits": {
          "total": 2706,
          "max_score": 1,
          "hits": [
            {
              "_index": "apm-retmon",
              "_type": "_doc",
              "_id": "FyUIoXgBJTwroTEjoWCu",
              "_score": 1,
              "_source": {
                "@timestamp": "2021-04-05T07:56:40.636197100Z",
                "hostname": "SIMPHONY3",
                "client.geo.location": "41.378197,-81.462354",
                "ServiceName": "POS_Application",
                "ServiceSummary": "Xstore Application is down ",
                "ServiceStatus": "2",
                "labels.OrgId": "1000",
                "labels.Country": "US",
                "labels.StoreNum": "101",
                "labels.LatLong": "41.378197,-81.462354",
                "labels.RegisterNum": "2",
                "labels.OpType": "Availability",
                "OrgHier": {
                  "OrgId": 1000,
                  "RegsterNum": "2",
                  "Store": "101",
                  "District": "1",
                  "Region": "West"
                },
                "labels.AppType": "xstore",
                "labels.AlertFlag": "No",
                "StatusChangeTime": "2021-04-05T07:19:31.034Z",
                "labels.Age": "37",
                "ServiceDetail": [
                  {
                    "Xstore": "OFFLINE",
                    "JmxPort": "2020",
                    "ConnectionToPort": "OFFLINE"
                  }
                ]
              },
              "OrgId": "1000",
              "StoreNum": "101",
              "RegisterNum": "2",
              "Region": "West"
            }
          ]
        },
        "aggregations": {"time_buckets": {"buckets": []}}
      }
    },
    {
      "source": "table",
      "name": "transformation",
      "transform": [
        {
          "type": "formula",
          "as": "id",
          "expr": "datum.key == 'OrgId' ? datum.OrgId : datum.key == 'Region' ? join([datum.OrgId,datum.Region],'-') : datum.key == 'StoreNum' ? join([datum.OrgId, datum.Region, datum.StoreNum],'-') : datum.key == 'RegisterNum' ? join([datum.OrgId, datum.Region, datum.StoreNum, datum.RegisterNum],'-') : null"
        },
        {
          "type": "formula",
          "as": "parent",
          "expr": "datum.key == 'OrgId' ? null : datum.key == 'Region' ? datum.OrgId : datum.key == 'StoreNum' ? join([datum.OrgId, datum.Region],'-') : datum.key == 'RegisterNum' ? join([datum.OrgId, datum.Region, datum.StoreNum],'-') : null"
        },
        {"type": "filter", "expr": "isDefined(datum.value)"},
        {"type": "aggregate", "groupby": ["id", "parent"]},
        {"type": "formula", "as": "label", "expr": "peek(split(datum.id,'-'))"}
      ]
    },
    {
      "name": "tree",
      "source": "transformation",
      "transform": [
        {"type": "stratify", "key": "id", "parentKey": "parent"},
        {
          "type": "tree",
          "method": {"signal": "layout"},
          "size": [{"signal": "height"}, {"signal": "width - 100"}],
          "separation": {"signal": "separation"},
          "as": ["y", "x", "depth", "children"]
        }
      ]
    },
    {
      "name": "links",
      "source": "tree",
      "transform": [
        {"type": "treelinks"},
        {
          "type": "linkpath",
          "orient": "horizontal",
          "shape": {"signal": "links"}
        }
      ]
    }
  ],
  "scales": [
    {
      "name": "color",
      "type": "linear",
      "range": {"scheme": "magma"},
      "domain": {"data": "tree", "field": "depth"},
      "zero": true
    }
  ],
  "marks": [
    {
      "type": "path",
      "from": {"data": "links"},
      "encode": {
        "update": {"path": {"field": "path"}, "stroke": {"value": "#ccc"}}
      }
    },
    {
      "type": "symbol",
      "from": {"data": "tree"},
      "encode": {
        "enter": {"size": {"value": 100}, "stroke": {"value": "#fff"}},
        "update": {
          "x": {"field": "x"},
          "y": {"field": "y"},
          "fill": {"scale": "color", "field": "depth"}
        }
      }
    },
    {
      "type": "text",
      "from": {"data": "tree"},
      "encode": {
        "enter": {
          "text": {"field": "label"},
          "fontSize": {"value": 9},
          "baseline": {"value": "middle"}
        },
        "update": {
          "x": {"field": "x"},
          "y": {"field": "y"},
          "dx": {"signal": "datum.children ? -7 : 7"},
          "align": {"signal": "datum.children ? 'right' : 'left'"},
          "opacity": {"signal": "labels ? 1 : 0"}
        }
      }
    }
  ],
  "config": {
    "range": {"category": {"scheme": "elastic"}},
    "arc": {"fill": "#54B399"},
    "area": {"fill": "#54B399"},
    "line": {"stroke": "#54B399"},
    "path": {"stroke": "#54B399"},
    "rect": {"fill": "#54B399"},
    "rule": {"stroke": "#54B399"},
    "shape": {"stroke": "#54B399"},
    "symbol": {"fill": "#54B399"},
    "trail": {"fill": "#54B399"},
    "title": {"color": "#343741"},
    "style": {
      "guide-label": {"fill": "#69707d"},
      "guide-title": {"fill": "#343741"},
      "group-title": {"fill": "#343741"},
      "group-subtitle": {"fill": "#343741"}
    },
    "axis": {
      "tickColor": "#eef0f3",
      "domainColor": "#eef0f3",
      "gridColor": "#eef0f3"
    },
    "background": "transparent"
  },
  "autosize": {"type": "fit", "contains": "padding"}
}