### 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
blink::SchemeRegistry::RegisterURLSchemeAsBypassingContentSecurityPolicy(
      extension_scheme);
  
  std::vector<std::string> secure_schemes_list =
      ParseSchemesCLISwitch(command_line, switches::kSecureSchemes);
  for (const std::string& scheme : secure_schemes_list)
    blink::SchemeRegistry::RegisterURLSchemeAsSecure(
        WTF::String::FromUTF8(scheme.data(), scheme.length()));
  std::vector<std::string> fetch_enabled_schemes =
      ParseSchemesCLISwitch(command_line, switches::kFetchSchemes);
  for (const std::string& scheme : fetch_enabled_schemes) {
    blink::WebSecurityPolicy::RegisterURLSchemeAsSupportingFetchAPI(
        blink::WebString::FromASCII(scheme));
  }
  std::vector<std::string> service_worker_schemes =
      ParseSchemesCLISwitch(command_line, switches::kServiceWorkerSchemes);
  for (const std::string& scheme : service_worker_schemes)
    blink::WebSecurityPolicy::RegisterURLSchemeAsAllowingServiceWorkers(
        blink::WebString::FromASCII(scheme));
  std::vector<std::string> csp_bypassing_schemes =
      ParseSchemesCLISwitch(command_line, switches::kBypassCSPSchemes);
  for (const std::string& scheme : csp_bypassing_schemes)
    blink::SchemeRegistry::RegisterURLSchemeAsBypassingContentSecurityPolicy(
        WTF::String::FromUTF8(scheme.data(), scheme.length()));
  
  
  blink::WebSecurityPolicy::RegisterURLSchemeAsAllowingServiceWorkers("file");
  blink::SchemeRegistry::RegisterURLSchemeAsSupportingFetchAPI("file");
#if defined(OS_WIN)