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Thanks for the report and patch.
I just tested that When the executable itself is symlinked (not installed, just linked from an existing installation), sys.exec_prefix and sys.executable are different. This means that a unit test (to prevent regressions) will be easy to write with the helpers in test.test_support (2.7)/test.support (3.x)/distutils2.tests.support.
os.path.samefile is not supported on Windows before 3.2; I guess we’ll have to live with that bug and just document it :(
Do you want to add tests for this? I’ll do it if you don’t.
(Out of curiosity, why are there three signed-off-by lines? Is there a secret community of distutils bug fixers using git?)