I have contacted Estimote team and they replied with the solution for registering the estimote beacons, It works I have tested..!
In order to register the beacon with Google's Beacon Tools, you'll need to disable all of the packets on the beacon (including Eddystone packets), then turn on the Eddystone Configuration Service. After that, you should see the beacon in the Beacon Tools app in the Unregistered section.
You will need to provide a key to register the beacon through the app. It's 00000000000000000000000000000000, and you may change it later, once the beacon's registered.