Firstly you won't want to be using `--target=wasm64` at all right now, it is experimental and not supported by any engines yet. Lucky `em++ --cflags` is going to contain its own `--target=wasm32-unknown-emscripten` so that is probably unrelated to your current failure.
Secondly, if you want emcc to produce bitcode you can simply add `-emit-llvm` to you normal emcc command:
em++ -c -emit-llvm -S <file>.cpp -o <file>.ll
or
em++ -c -emit-llvm <file>.cpp -o <file>.bc
If you want to combine the bitcode files into a single large bitcode file we do also still have legacy support for that via the `-r` + `-flto` flags.
em++ -r -flto <file1>.bc <file2>.bc -o whole-program.bc
But this kind of bitcode linking has some caveats and I would not recommend it. Avoid it if you can.
cheers,
sam