There's no reason at all why not.
The only minor issue is that Q2A retrieves some information (but not the full content) for all the pages in the database for every page view, in order to build the navigation menus, so this could end up being quite a bit of data, most of which isn't necessary because not all the pages have navigation links.
You can resolve this by making the following change to function qa_db_pages_selectspec() in qa-db-selects.php:
'source' => '^pages ORDER BY position',
.... to ...
'source' => "^pages WHERE nav IN ('M', 'O', 'F', 'B') ORDER BY position",
That means information will only be retrieved about those pages which have a navigation link. And if you want to make this query more efficient, add an INDEX on the nav column in the qa_pages table.