The original problem was that when filtering two levels up in
inheritance chain, Django optimized the join generation so that the
middle model was skipped. But then Django generated joins from top
to middle to bottom for SELECT clause, and thus there was one extra
join (top->middle->bottom + top -> bottom).

This case is fixed in master as the filtering optimization is gone.
This has the side effect that in some cases there is still extra join
if the SELECT clause doesn't contain anything from middle or bottom.