### 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/renderer_client_base.cc
v8::Isolate* isolate,
    v8::Local<v8::Object> binding_object) {
  mate::Dictionary dict(isolate, binding_object);
}
void RendererClientBase::RenderThreadStarted() {
  auto* command_line = base::CommandLine::ForCurrentProcess();
#if BUILDFLAG(USE_EXTERNAL_POPUP_MENU)
  
  
  
  if (command_line->HasSwitch(options::kOffscreen)) {
    blink::WebView::SetUseExternalPopupMenus(false);
  }
#endif
  blink::WebCustomElement::AddEmbedderCustomElementName("webview");
  blink::WebCustomElement::AddEmbedderCustomElementName("browserplugin");
  WTF::String extension_scheme("chrome-extension");
  
  
  blink::SchemeRegistry::RegisterURLSchemeAsSupportingFetchAPI(
      extension_scheme);
  
  
  blink::SchemeRegistry::RegisterURLSchemeAsFirstPartyWhenTopLevel(
      extension_scheme);
  
  
  blink::SchemeRegistry::RegisterURLSchemeAsSecure(extension_scheme);