I believe the problem here has nothing to do with the XML, but the SQL. The difference is that the query that doesn't work explicitly selects "container.name", while the query that does work selects "container". Note, that the .xml file applies metadata to the _result_ of the query. So the lookup defined in the .xml is not available to the SQL in the .sql file. This explains why container.name is not valid.

Note that the lookup is available/known by the data region which is why the GEE_studyCohortsInfo grid displays name.