There are limits to what the commandline arguments can take. And even if you fallback to files instead, you still need to serialise a potentially huge amount of data. (Wanna serialise a 1GB tree that is going to get only one lookup in each call to the script?) On top of that, you're missing any chance of in-memory caching, because the script call can't preserve that, while FFI could. Then there are things that are just not possible to serialise like pointers to mapped memory, file descriptors (outside of unix sockets), etc.

Finally even if everything works, a command execution and parsing results is massively slower than a function call. So yeah, there's lots of restrictions on what you can practically do that way.