I think my main objection is that these query methods should conceptually be on the QuerySet, and so defining them on the Manager (the "wrong place") and magically copying them to the QuerySet (the "right place") feels somehow worse than the opposite.
I appreciate that you raised the discussion on the mailing list, as it highlights the fact that this is a common problem in big Django codebases. Even pulling something like PassThroughManager into core might work (perhaps with a nicer "manager_with_queryset" API, as suggested by Aramgutang).