The fielded systems require something that wasn't there in the original model of zero-knowledge proofs. That could be as little as a trusted-enough public source of randomness: the prover makes their initial commitments, plays the verification game with a verifier whose challenges are controlled by the next outputs of the public RNG, and as long as the other party trusts that the RNG and prover aren't in cahoots, that's enough. Doing a trusted setup process beforehand is another tool used by a bunch of deployed systems.

That doesn't mean anything's practically wrong with the fielded ZK proof systems, just that's how you reconcile the article's "no non-interactive proofs under these assumptions" with people out in the real world using non-interactive proofs.

This paper brings up another logical possibility, that there could be a non-interactive proof with no RNG or setup that doesn't meet the precise original definition of zero-knowledge proofs but is zero-knowledge practically speaking. I don't know whether we'll actually see better fielded ZK proof systems come out of this approach!