Vlad Is the Helium browser a valid example? You can't minimize it to the stage manager and thus it won't break it.
I saw that @eirk posted a suggestion that Webapps should be useable from the menubar. In this case minimizing it to the stage manager wouldn't make sense anymore, right?
Just as it currently is, it breaks the stage manager and the only thing I can do once it does is quiting the Webapp.