You're assuming that all code can be trusted. Jsonnet is much easier to make secure than JS, since it can be statically guaranteed to be safe and side-effect-free (e.g. can't access the file system). This permits evaluating arbitrary untrusted data, which can be a boon to systems like CI servers, databases, or even Kubernetes (think Helm charts).
The script to generate that JSON is code. Jsonnet also generates JSON. So his script is filling the same role as Jsonnet would. The point stands.
He might trust his code, but I was highlighting reasons why this is not true everywhere, and indeed the ability to evaluate untrusted code can open up previously unavailable avenues. For example, storing server-side Jsonnet that can be safely evaluated by a multitenant backend.