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FWIW, I also explored my original proposal, which essentially moved the above script and modifications into the Python configure.ac and Makefile.pre.in files, so that Python's internal build process would create the native build system versions of Python and Parser/pgen, if necessary. I made some progress in creating additional Make targets just for the native build system, which redefined the toolchain after completion; however, I encountered unexepected, overwhelming configure contamination in the auto-generated header files.
Maybe someone can push this farther than me? I'm attaching my patch, in case it helps someone else and just as reference.
As for me, I think it is much easier to use the above solution, which would require very little patching to the sources to make a 2-step compilation to be trivial.