If building in a path that starts with /usr, the includedir=$(echo "@includedir@" | sed "s#^$prefix_build#$prefix_real#") assignment in the python-config.sh ends up having the path it processes ran through a path substitution once before this line is executed because the @includedir@ in the python-config.sh.in is set to the string '${prefix}/include'.  ${prefix} is assigned just above includedir in python-config.sh to prefix=$(echo "$prefix_build" | sed "s#^$prefix_build#$prefix_real#")

I believe we need to update the line ref below to 

includedir=$(echo "@includedir@")

https://git.busybox.net/buildroot/tree/package/python3/0010-Misc-python-config.sh.in-ensure-sed-invocations-only.patch#n43

Another option would be to rename the prefix variable in this file so that there isn't a naming conflict......

Example build failure
http://autobuild.buildroot.net/results/dfd/dfdac93d25d5730f08aa747e615a1a1c3ac7f1c0/