I use Polylang plugin for multilangual blog.
Structure of permalinks: %postname.html (site.com/post.html for posts and site.com/page for pages). I have tried WordPress Seo 126.96.36.199.
All main pages on different languages, such as site.com/en or site.com/de, have same canonical URL - site.com and not indexes.
Also this pages don't fall to sitemap.xml