When inserting a link from SharePoint in Rich Text Editor SharePoint uses the physical URL of the selected page in the hyperlink even if that page has a Friendly URL configured.
At the upcoming SharePoint Connect 2014 I will be speaking on building SharePoint 2013 portals and public-facing websites using the Single Page App approach.
Mavention Insert Table of Contents is now available as an App for SharePoint.
On your public-facing website use the XML Sitemap and Robots.txt file to optimize your website for Internet search engines.
When using Device Channels on your website set the Vary: User-Agent response header to let Internet search engines know that different HTML is rendered to different browsers.