Ah, no, Atarim is not meant as an replacement for the existing docu. It would be similar to a overlay over the existing docu, where users can propose changes (text, images, files), and the admin get them in his dashboard in a list, and can directly jump to the existing page. I guess you misinterpreted the functionality of atarim. It should serve only as an information system, where users can propose changes to the existing docu. It would not change or replace in any kind the docu itself. The changes still must be done from the admins as they are done now.
So there is no risk to run in limitations. Docu is handled as it was before. What is written in the docu stays written in the docu. Its previous name was WP Feedback, it was previous a wp only plugin. Now its self-standing (atarim-hosted) and can handle any website. It does NOT need any plugins or accounts or API or other direct connection.
Recognition from parts of the website is similar to Browser Inspector, or Firebug, or CSS Hero, but grafically, and you get a textfield and more tools at this element, when you point the mouse there - then you write your suggestions. If sended, admin will get notification and your comments (and files/screenshots,..) in his dashboard. To make the changes is and stays in docu-admins hands.