Access to Chrome via the System Tray should go through the User Manager.

chrome/browser/resources/user_manager/user_manager.js

 // Copyright 2013 The Chromium Authors. All rights reserved.
 // Use of this source code is governed by a BSD-style license that can be
 // found in the LICENSE file.
 <include src="../../../../ui/login/screen.js">
 <include src="../../../../ui/login/bubble.js">
 <include src="../../../../ui/login/login_ui_tools.js">
 <include src="../../../../ui/login/display_manager.js">
 <include src="control_bar.js">
 <include src="../../../../ui/login/account_picker/screen_account_picker.js">
 <include src="../../../../ui/login/account_picker/user_pod_row.js">
@@ skipping 120 matching lines @@
   function initialize() {
     cr.ui.login.DisplayManager.initialize();
     cr.ui.login.UserManagerTutorial.initialize();
     login.AccountPickerScreen.register();
     cr.ui.Bubble.decorate($('bubble'));
     login.HeaderBar.decorate($('login-header-bar'));
 
     // Hide the header bar until the showUserManagerMethod can apply function
     // parameters that affect widget visiblity.
     $('login-header-bar').hidden = true;
-    chrome.send('userManagerInitialize');
+
+    var hash = window.location.hash;
+    if (hash)
+      chrome.send('userManagerInitialize', [hash]);
+    else
+      chrome.send('userManagerInitialize');

[Evan Stade, 2014/09/11 17:02:50]

chrome.send('userManagerInitialize', [window.location.hash]);

[Mike Lerman, 2014/09/11 18:49:29]

Done.

   }
 
   // Return an object with all of the exports.
   return {
     initialize: initialize
   };
 });
 
 var Oobe = cr.ui.Oobe;
 
 // Allow selection events on components with editable text (password field)
 // bug (http://code.google.com/p/chromium/issues/detail?id=125863)
 disableTextSelectAndDrag(function(e) {
   var src = e.target;
   return src instanceof HTMLTextAreaElement ||
          src instanceof HTMLInputElement &&
          /text|password|search/.test(src.type);
 });
 
 document.addEventListener('DOMContentLoaded', UserManager.initialize);