* Electron version: 1.7.1
* Operating system: MacOS

### Expected behavior

The popup should have `window.opener` set

### Actual behavior

I was using native `window.open` in sandbox mode until this PR was merged : https://github.com/electron/electron/pull/8963

I switched to non-sandbox mode using the version 1.7.1 and what happen is that, if your main app is embedded in an iframe and if it open a new window using `window.open`, the new window won't have `window.opener` set

If I load the same app directly in the main window and not using the iframe, it is working as expected

I am using the code from https://github.com/electron/electron/blob/master/docs/api/window-open.md

### How to reproduce

In the main window load in an iframe your app.

In the app open a popup with `window.open`

The new popup does not have `window.opener` set
atom/browser/atom_browser_client.cc
const content::MainFunctionParams&) {
  v8::V8::Initialize();  
  return new AtomBrowserMainParts;
}
void AtomBrowserClient::WebNotificationAllowed(
    int render_process_id,
    const base::Callback<void(bool, bool)>& callback) {
  content::WebContents* web_contents =
      WebContentsPreferences::GetWebContentsFromProcessID(render_process_id);
  if (!web_contents) {
    callback.Run(false, false);
    return;
  }
  auto permission_helper =
      WebContentsPermissionHelper::FromWebContents(web_contents);
  if (!permission_helper) {
    callback.Run(false, false);
    return;
  }
  permission_helper->RequestWebNotificationPermission(
      base::Bind(callback, web_contents->IsAudioMuted()));
}
void AtomBrowserClient::RenderProcessHostDestroyed(