This issue is *really* annoying: it makes buildbots almost useless (it is no more possible to check if a commit introduces a regression). So until the best fix is decided, I applied a temporary fix (based on  changes.diff written by  Vinay Sajip):

New changeset 2a9e1eb3719c by Victor Stinner in branch 'default':
Issue #18081: Workaround "./python -m test_idle test_logging" failure
http://hg.python.org/cpython/rev/2a9e1eb3719c

I checked that "import warnings; warnings.warn('test')" does still use the custom warning hook in IDLE. I don't know how to test all hooks.