Kibana3Beta4 seems to have changed around the UI a bit, enforcing query and filter bars up top. This is more opinionated that previous versions, which were more configurable (although potentially more confusing).
It would still be nice to be able to add a query panel elsewhere in the grid layout, even if it has the same functionality as the query bar. This seems to work fine in the code, although the 'query' panel does not appear in the add-panel dropdown. It would be nice to give that flexibility back to the user.