### Preflight Checklist
* [x] I have read the [Contributing Guidelines](https://github.com/electron/electron/blob/master/CONTRIBUTING.md) for this project.
* [x] I agree to follow the [Code of Conduct](https://github.com/electron/electron/blob/master/CODE_OF_CONDUCT.md) that this project adheres to.
* [x] I have searched the issue tracker for an issue that matches the one I want to file, without success.

### Issue Details

* **Electron Version:**
  5.0.1
* **Operating System:**
  windows
* **Last Known Working Electron version:**
  n/a

### Expected Behavior
A preload script should run only 1 time for each webContents / iframe

### Actual Behavior
The preload script appears to run multiple times

### To Reproduce
https://github.com/Tim91084/electron-node-subframe-issue/tree/node-in-subframe-runs-too-often

```sh
$ git clone https://github.com/Tim91084/electron-node-subframe-issue.git -b node-in-subframe-runs-too-often
$ npm install
$ npm start || electron .
```

### Screenshots
![image](https://user-images.githubusercontent.com/5086428/58273769-63b9d900-7d5f-11e9-8d30-1525dea34ce3.png)

shell/renderer/atom_renderer_client.cc
: node_bindings_(
          NodeBindings::Create(NodeBindings::BrowserEnvironment::RENDERER)),
      electron_bindings_(new ElectronBindings(uv_default_loop())) {}
AtomRendererClient::~AtomRendererClient() {
  asar::ClearArchives();
}
void AtomRendererClient::RenderFrameCreated(
    content::RenderFrame* render_frame) {
  new AtomRenderFrameObserver(render_frame, this);
  RendererClientBase::RenderFrameCreated(render_frame);
}
void AtomRendererClient::RunScriptsAtDocumentStart(
    content::RenderFrame* render_frame) {
  
  v8::HandleScope handle_scope(v8::Isolate::GetCurrent());
  node::Environment* env = GetEnvironment(render_frame);
  if (env)
    mate::EmitEvent(env->isolate(), env->process_object(), "document-start");
}
void AtomRendererClient::RunScriptsAtDocumentEnd(
    content::RenderFrame* render_frame) {
  
  v8::HandleScope handle_scope(v8::Isolate::GetCurrent());
  node::Environment* env = GetEnvironment(render_frame);
  if (env)
    mate::EmitEvent(env->isolate(), env->process_object(), "document-end");
}
void AtomRendererClient::DidCreateScriptContext(