Ultimately you're right that npm doesn't work well to manage the situation Zod finds itself in. But Zod is subject to a bunch of constraints that virtually no other libraries are subject to. There are dozens or hundreds of libraries that directly import interfaces/classes from "zod" and use them in their own public-facing API.
Since these libraries are directly coupled to Zod, they would need to publish a new major version whenever Zod does. That's ultimately reasonable in isolation, but in Zod's case it would trigger a "version avalanche" would just be painful for everyone involved. Selfishly, I suspect it would result in a huge swath of the ecosystem pinning on v3 forever.
The approach I ended up using is analogous to what Golang does. In essence a given package never publishes new breaking versions: they just add a new subpath when a new breaking release is made. In the TypeScript ecosystem, this means libraries can configure a single peer dependency on zod@^3.25.0 and support both versions simultaneously by importing what they need from "zod/v3" and "zod/v4". It provides a nice opt-in incremental upgrade path for end-users of Zod too.