Are we sure that the base reveals nothing about the factors if n is composite? I have never seen a proof of that.
Usually, zero knowledge proofs also require a prover who knows the answer (the factors in this case). This is just a primality test that can be performed locally.
We also don't technically have proofs for some of the computational hardness assumptions that popular "real" ZK proof constructions rely on!
This might feel different because those assumptions were chosen in part because people had studied them and they certainly seem to be right, whereas perhaps here nobody has really studied this particular random number theory topic one way or the other.
But in some sense, there isn't a proof that regular ZK proof methods are actually completely zero-knowledge (against a computationally bounded adversary).
My understanding is that there is a difference between the concept of a Zero-Knowledge Proof (ZKP), and then the applications that such a thing is possible.
In the example given, I can prove that N is composite without revealing anything (well, almost anything) about the factors. But in practice we want to use a ZKP to show that I have specific knowledge without revealing the knowledge itself.
For example:
You can give me a graph, and I can claim that I can three-colour it. You may doubt this, but there is a process by which I can ... to any desired level of confidence ... demonstrate that I have a colouring, without revealing what the colouring is. I colour the vertices RGB, map those colours randomly to ABC, and cover all the vertices. You choose any edge, and I reveal the "colours" (from ABC) of the endpoints. If I really can colour the graph then I will always be able to reveal two different colours. If I can't colour the graph then as we do this more and more, eventually I will fail.
So you are right, but the message of the post is, I think, still useful and relevant.