I have not tested this yet, but it appears that copy/copyIndex should now be a supported scenario for traffic manager endpoints:
https://feedback.azure.com/forums/217313-networking/suggestions/12907815-support-copy-copyindex-in-traffic-manager-depend
Here is a sample that I implemented a while back:
{
  "$schema": "https://schema.management.azure.com/schemas/2015-01-01/deploymentTemplate.json#",
  "contentVersion": "1.0.0.0",
  "parameters": {
    "solution-abbreviation": {
      "type": "string",
      "minLength": 1
    },
    "environment-abbreviation": {
      "type": "string",
      "allowedValues": [
        "dev",
        "test",
        "prod"
      ]
    },
    "userinterface-abbreviation": {
      "type": "string",
      "minLength": 1
    },
    "userinterface-locations": {
      "type": "array",
      "minLength": 1
    },
    "userinterface-appserviceplan-sku": {
      "type": "string",
      "allowedValues": [
        "Free",
        "Shared",
        "Basic",
        "Standard"
      ]
    },
    "userinterface-appserviceplan-workersize": {
      "type": "string",
      "allowedValues": [
        "0",
        "1",
        "2"
      ]
    },
    "userinterface-appserviceplan-numberofworkers": {
      "type": "int"
    }
  },
  "variables": {
    "userinterface-trafficmanager-name": "[concat(parameters('solution-abbreviation'), '-', parameters('environment-abbreviation'), '-', parameters('userinterface-abbreviation'))]"
  },
  "resources": [
    {
      "name": "[concat(variables('userinterface-trafficmanager-name'), '-', parameters('userinterface-locations')[copyIndex()])]",
      "type": "Microsoft.Web/serverfarms",
      "location": "[parameters('userinterface-locations')[copyIndex()]]",
      "apiVersion": "2014-06-01",
      "dependsOn": [ ],
      "tags": {
        "displayName": "[concat(variables('userinterface-trafficmanager-name'), '-', parameters('userinterface-locations')[copyIndex()])]"
      },
      "copy": {
        "name": "[concat('serverfarms', '-copy')]",
        "count": "[length(parameters('userinterface-locations'))]"
      },
      "properties": {
        "name": "[concat(variables('userinterface-trafficmanager-name'), '-', parameters('userinterface-locations')[copyIndex()])]",
        "sku": "[parameters('userinterface-appserviceplan-sku')]",
        "workerSize": "[parameters('userinterface-appserviceplan-workersize')]",
        "numberOfWorkers": "[parameters('userinterface-appserviceplan-numberofworkers')]"
      }
    }
  ],
  "outputs": {
  }
}