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The compiler needs specific exemptions because parts of the GPLed runtime libraries are included in all compiled code. No part of the autotools ends up in the finished code. If it did, you would need m4 to run Python and you don't.
It doesn't matter whether it ends up in the finished code: if the aclocal.m4 is indeed GPL-licensed, then the entire Python source distribution must be GPL-licensed, because it "contains or is derived from the Program or any part thereof".
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