Catch-22: Running bootstrap.py requires Binaryen in config, but it's not there until having installed Emscripten

I realize now my PR https://github.com/emscripten-core/emsdk/pull/1444 is botched up.

When run on a clean installation (git clone and then `emsdk install sdk-main64bit`), the bootstrap.py step fails, because it needs to see .emscripten_config generated to find Binaryen.

But .emscripten_config cannot be generated until the SDK has been installed and activated. Need to figure something else out.

For Unity use, we absolutely cannot have the bootstrap.py functionality at all: Emscripten will be installed into a read-only directory in the filesystem, so everything is frozen. So it is desirable to be able to have emsdk run bootstrap.py in some form during installation stage.