Sure, nothing stops you from using a DTO layer in Seam. I'm not quite sure I understand what you are asking?
I think the question is confusing because I have several symptoms and I'm looking for one cause. I assumed not directly injecting the entity manager into my action listener beans was the cause of a problem. But if I'm using an extended persistence context, the persistence context should always last the length of the conversation no matter where in the code its being injected, right?
Now I think my issue was that some of my code was using the old way of getting an entity manager and creating from a JNDI looked up EMF. I assumed that because I was not using transactions directly or even modifying data, where I got the EM didn't really matter. Seam really didn't like this or something I was doing (kept destroying stateful beans before the conversation ended) and many problems resulted with using things like @DataModel and in parameter redirection. For some reason, I was able to get around this by creating a fake long running conversation even though it wasn't really needed. However, this is coming back to bite me as I'm adding admin features and data isn't being updated in the db.
I guess I'd like to know if my thoughts even make sense and more specifically, if there's a relationship between the EM and how Seam ends conversations.