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I gave it a shot and this commit: https://github.com/t0m/hibernate-orm/commit/f50a372c6cd46216f9928afd1ad2cabb00599b80 passes the test suite and fixes mine and Tony's test cases. This doesn't affect Grzegorz's problem w/r/t scalars in an hql query, so I think we have two separate issues.
For the fix, I added a separate suffix array for collections that are loaded by inner join. When it comes time to create the select fragment, it passes in either the outer join suffix or the inner join suffix depending on the join type. I'm not familiar with hibernate internals so this is just a quick hack (a.k.a. don't use this for anything) but hopefully it helps out in developing a more robust fix.