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It turns out this is pretty easy to fix by just changing the stub to import builtins or __builtin__ depending on the python install version. Attached are patches that fix this for both the default and 2.7 branches.
My test case is a pure python module with an install script. I've rebuilt the wininst stub for both default (3.3) with VS2010 Express and 2.7 with VS2008 Express. I then built installers and ran them in both directions: installer created with python-2.7 and installed into python-3.3, and an installer created with python-3.3 and installed into python-2.7. Both worked fine with no warnings.
I've attached the stubs I built in case they're helpful. wininst-10.0-compat.exe is the 32 bit stub for default/3.3. wininst-9.0-compat-2.7.exe is the 32 bit stub for 2.7.