The real issue here is that the test used to determine whether -S was passed or not is outdated: instead of checking sys.flags.no_site, it checks whether 'site' is in sys.modules.  This is no longer a valid test, since site's side effects are contained within site.main, which is only run if no_site is False.  In fact, distutils imports symbols from site unconditionally, as do a couple of test modules; hence why test_site currently fails running `python -S Lib/test`: test_distutils (and others) run before test_site and cause site to be present in sys.modules.

I think we should move away from a toplevel SkipTest, though; some of the tests may be applicable whether -S is passed or not, though of course the ImportSideEffectTests would not be.