### 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
if (!node::tracing::TraceEventHelper::GetAgent())
    node::tracing::TraceEventHelper::SetAgent(node::CreateAgent());
  
  v8::Local<v8::Context> context =
      node::MaybeInitializeContext(renderer_context);
  DCHECK(!context.IsEmpty());
  node::Environment* env = node_bindings_->CreateEnvironment(context);
  auto* command_line = base::CommandLine::ForCurrentProcess();
  
  
  if (command_line->HasSwitch(switches::kDisableElectronSiteInstanceOverrides))
    env->ForceOnlyContextAwareNativeModules();
  env->WarnNonContextAwareNativeModules();
  environments_.insert(env);
  
  electron_bindings_->BindTo(env->isolate(), env->process_object());
  AddRenderBindings(env->isolate(), env->process_object());
  mate::Dictionary process_dict(env->isolate(), env->process_object());
  process_dict.SetReadOnly("isMainFrame", render_frame->IsMainFrame());
  
  node_bindings_->LoadEnvironment(env);
  if (node_bindings_->uv_env() == nullptr) {
    
    node_bindings_->set_uv_env(env);
    
    node_bindings_->RunMessageLoop();
  }
}
void AtomRendererClient::WillReleaseScriptContext(