Secure multi-party private set intersectio: Protocols supporting MULTI-party VS supporting TWO-party
I think that you are mixing between the terms "applications" and "implementation", let me explain.

In your question you took some secure two-party computation (2PC) and you showed that when using it in a "black-box" fashion and also each party gets the result of the computation on each pair of the inputs then the protocol leaks a lot of information that should not be leaked. This is true. But it doesn't mean that a secure multi-party computation (MPC) is useless! It just simply means that the protocol that you described (using 2PC) is leaking information and thus it is not secure!.

This multiparty set intersection is INDEED an application for MPC, it is just not implemented as you said but has some designated protocol that implements it (not necessarily through 2PC).

I hope that it clarifies the things.