### 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
#include "third_party/blink/public/web/web_custom_element.h"  
#include "third_party/blink/public/web/web_frame_widget.h"
#include "third_party/blink/public/web/web_plugin_params.h"
#include "third_party/blink/public/web/web_script_source.h"
#include "third_party/blink/public/web/web_security_policy.h"
#include "third_party/blink/public/web/web_view.h"
#include "third_party/blink/renderer/platform/weborigin/scheme_registry.h"  
#if defined(OS_MACOSX)
#include "base/strings/sys_string_conversions.h"
#endif
#if defined(OS_WIN)
#include <shlobj.h>
#endif
#if BUILDFLAG(ENABLE_PDF_VIEWER)
#include "shell/common/atom_constants.h"
#endif  
#if BUILDFLAG(ENABLE_PEPPER_FLASH)
#include "chrome/renderer/pepper/pepper_helper.h"
#endif  
#if BUILDFLAG(ENABLE_TTS)
#include "chrome/renderer/tts_dispatcher.h"
#endif  
#if BUILDFLAG(ENABLE_PRINTING)
#include "components/printing/renderer/print_render_frame_helper.h"
#include "printing/print_settings.h"
#include "shell/renderer/printing/print_render_frame_helper_delegate.h"
#endif  
namespace electron {
namespace {
std::vector<std::string> ParseSchemesCLISwitch(base::CommandLine* command_line,