Figured it out. I had to pass the environment variable on the command line to configure.
I’m using Ethan’s scripts to build. I modified the build-python-emscripten-node.sh to be like so:
CONFIG_SITE=../../Tools/wasm/config.site-wasm32-emscripten \
emconfigure ../../configure -C \
--host=wasm32-unknown-emscripten \
--with-pydebug \
PKG_CONFIG_PATH=/home/rich/source/libffi-emscripten \ <-- This line
--enable-wasm-pthreads=yes \
--build=$(../../config.guess) \
--with-emscripten-target=node \
--enable-wasm-dynamic-linking=no \
--with-build-python=$(pwd)/../build/python \
"$@"
With of course building the libffi-emscripten repo first.