It looks like the now recommended compiler backend for emscripten is the upstream LLVM instead of fastcomp + asm2wasm (WebAssembly/binaryen#2177 (comment)).

This might also help with scipy dynamic linking, as the section of code that errors now in #473 will no longer be run.

There is no tagged emsdk release with it yet, I think, but hopefully, one be released soon.

I don't have a very good understanding of how much work this would involve. I'm hoping existing emsdk patches would still apply. Maybe it would be necessary to update to the latest emsdk release first.