Emscripten people helped me out here. It seems that the flag needs to be set at the final step of compilation, when the .html file is generated. The PROJECT_CFLAGS are only using the flag when .cpp files are compiled.
I couldn't figure out how to automate this using config.make, but I was able to get it working by repeating the .html compilation step after emmake make finishes, and adding on the flag I want.
It looks like this:
/Users/admin/bin/emsdk_portable/emscripten/1.35.0/em++ -o bin/myproject.html -O3 -s OUTLINING_LIMIT=100000 -s TOTAL_MEMORY=134217728 -s DISABLE_EXCEPTION_CATCHING=0 --memory-init-file 1 obj/emscripten/Release/src/animation.o obj/emscripten/Release/src/main.o obj/emscripten/Release/src/ofApp.o ../../../addons/obj/emscripten/Release/ofxEmscripten/src/ofxAppEmscriptenWindow.o ../../../addons/obj/emscripten/Release/ofxEmscripten/src/ofxEmscriptenSoundPlayer.o ../../../addons/obj/emscripten/Release/ofxEmscripten/src/ofxEmscriptenSoundStream.o ../../../addons/obj/emscripten/Release/ofxEmscripten/src/ofxEmscriptenURLFileLoader.o ../../../addons/obj/emscripten/Release/ofxEmscripten/src/ofxEmscriptenVideoGrabber.o ../../../addons/obj/emscripten/Release/ofxEmscripten/src/ofxEmscriptenVideoPlayer.o ../../../addons/obj/emscripten/Release/ofxJSON/src/ofxJSONElement.o ../../../addons/obj/emscripten/Release/ofxJSON/libs/jsoncpp/src/jsoncpp.o ../../../addons/obj/emscripten/Release/ofxLayerMask/src/ofxLayerMask.o ../../../addons/obj/emscripten/Release/ofxTexturePlane/src/ofxTexturePlane.o ../../../addons/obj/emscripten/Release/ofxAnimatable/src/ofxAnimatable.o ../../../addons/obj/emscripten/Release/ofxAnimatable/src/ofxAnimatableFloat.o ../../../addons/obj/emscripten/Release/ofxAnimatable/src/ofxAnimatableOfColor.o ../../../addons/obj/emscripten/Release/ofxAnimatable/src/ofxAnimatableOfPoint.o ../../../libs/openFrameworksCompiled/lib/emscripten/libopenFrameworks.bc -Wl,--as-needed -Wl,--gc-sections --preload-file bin/data@data --emrun --js-library ../../../addons/ofxEmscripten/libs/html5video/lib/emscripten/library_html5video.js --js-library ../../../addons/ofxEmscripten/libs/html5audio/lib/emscripten/library_html5audio.js --shell-file ../../../libs/openFrameworksCompiled/project/emscripten/template.html ../../../libs/FreeImage/lib/emscripten/libfreeimage.a ../../../libs/boost/lib/emscripten/libboost_filesystem.a ../../../libs/boost/lib/emscripten/libboost_system.a ../../../libs/tess2/lib/emscripten/libtess2.a ../../../libs/freetype/lib/emscripten/libfreetype.bcThanks
