Benny K J added the comment:

To eliminate the issues introduced by the native python on the Ubuntu 16.04 
host, I've set up a new Ubuntu Host with all the native python packages removed.

But now when I try to build the make fails saying:

arm-linux-gnueabihf-gcc -shared 
  -Wl,--no-as-needed -o -Wl,
  -Xlinker -export-dynamic -o python Programs/python.o -L. -lpython3.5m 
-lpthread -ldl  -lpthread -lutil   -lm  
_PYTHON_HOST_PLATFORM=linux-arm PYTHONPATH=./Lib:./Lib/plat-linux python -S -m 
sysconfig --generate-posix-vars ;\
if test $? -ne 0 ; then \
        echo "generate-posix-vars failed" ; \
        rm -f ./pybuilddir.txt ; \
        exit 1 ; \
/bin/sh: 1: python: not found
generate-posix-vars failed
Makefile:598: recipe for target 'pybuilddir.txt' failed
make: *** [pybuilddir.txt] Error 1

Looking at the configure.log it complains of missing python as well:

python: not-found! cannot run $(srcdir)/Parser/

Could you please comment if it is not possible to build python3 without first 
installing a native python on the build machine?

Maybe I have not set all the options to the ./configure correctly (e.g 


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