Instead of renaming QueryParams use a computed property

application.controller.js

import Ember from 'ember';

export default Ember.Controller.extend({
  appName:'Ember Twiddle'
});

application.route.js

import Ember from 'ember';

export default Ember.Route.extend({  
  beforeModel: function (transition) {
    this.transitionTo('test', {
      queryParams: {
        sidebar: true,
        footer: true
      }
    });
  }
});

application.template.hbs

{{outlet}}

router.js

import Ember from 'ember';
import config from './config/environment';

var Router = Ember.Router.extend({
  location: config.locationType
});

Router.map(function() {
  this.route('test');
});

export default Router;

test.controller.js

import Ember from 'ember';

export default Ember.Controller.extend({
  queryParams: [
    'sidebar',
    { isFooterVisible: { as: 'footer' } }
  ],
  sidebar: false,
  isFooterVisible: false
});

test.template.hbs

<h2>test/template.hbs</h2>

<p>This twiddle demonstrates an issue where renamed query params cause a problem when passed in a call to "transitionTo".</p>

<p>The application fails to load.</p>

sidebar?: {{#if sidebar}}Yes{{else}}No{{/if}}
<br>

isFooterVisible?: {{#if isFooterVisible}}Yes{{else}}No{{/if}}

twiddle.json

{
  "version": "0.4.6",
  "dependencies": {
    "jquery": "https://cdnjs.cloudflare.com/ajax/libs/jquery/1.11.3/jquery.js",
    "ember": "release",
    "ember-template-compiler": "release"
  }
}