I just realized that PYTHON_FOR_BUILD is far more complicated. Our WASM build system sets the env var to "$(pwd)/cpython/builddir/build/python". The configure script expects us to set several additional env vars.

The logic goes like this for cross compiling:

if PYTHON_FOR_BUILD is empty:
    find Python interpreter with same version as PACKAGE_VERSION
    set PYTHON_FOR_BUILD='_PYTHON_PROJECT_BASE=$(abs_builddir) _PYTHON_HOST_PLATFORM=$(_PYTHON_HOST_PLATFORM) PYTHONPATH=$(shell test -f pybuilddir.txt && echo $(abs_builddir)/`cat pybuilddir.txt`:)$(srcdir)/Lib _PYTHON_SYSCONFIGDATA_NAME=_sysconfigdata_$(ABIFLAGS)_$(MACHDEP)_$(MULTIARCH) '$interp
else:
    use user-supplied PYTHON_FOR_BUILD

Since we don't set any of the variables _PYTHON_PROJECT_BASE, _PYTHON_HOST_PLATFORM, and _PYTHON_SYSCONFIGDATA_NAME, we get wrong sysconfig data file.