Yeah pushing emscripten of Unity to new version is a best solution either, but I think it's impossible. They didn't change emscripten version for many years, they use 1.38.11. I don't know why, maybe there is some internal problem, but seems it's not into their priority. They still use js2wasm to generate WebAssembly.
I tried to update it manually by replacing emscripten, and hook into build scripts, however they also uses *.bc files to link into binary. As answered before, it's not possible to use *.bc files from older version of emscripten with newer emscripten.
So, I see back porting wasm-split is only solution, btw I hope it will not be super hard. I did similar stuff with js split. I use wasm file from unity and split out some functions into js, now I just want to improve my technology with wasm-split.