Actually, you're right on that. I don't know if that would per se be an issue, but now I recall that Toplink does not support SAME_TABLE, which kind of makes the first question moot.
In all truthfulness, if this idiom is not epidemic throughout your system, but rather isolated to this specific table (and it's subtables), I'd just make a specific exception for them in your DAO layer.
In our projects, we have a layer above the entity manager (via a session bean) that all of our data access goes through. In our case such a workaround would be straightforward, I don't know about your case.
You may consider looking at other JPA providers (Hibernate, Kodo, OpenJPA) as well, but I can't help you at all there having no experience with any of them.
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