The first one happens only when the person first allows your app. First time a person allows your app they will see the normal javascript dialogs. However, if they come back to your game, they will see the second dialog that occurs inside your game.
We prevent a normal click-through in our dialogs that should be enforced by Unity's Modal Window: https://docs.unity3d.com/Documentation/ScriptReference/GUI.ModalWindow.html
However, it looks like Unity has a bug on their end that might clicks through. I've messaged Unity and they are now aware of the issue. Thanks for reporting that.