Computers are boxes, therefore all software is literally (and figuratively) "in a box", are they not? This might seem like a frivolous jest, but it is not. For example, the author points out that clojure, java, kotlin can interoperate, but notes they are stuck in the same jvm 'box'. This generalizes and recurses, so you must find a specific place to stop, and then motivate that.

One likely place to stop is at "processes". But this must be motivated since ultimately processes are as synthetic a convention as a language thread - it's just that the runtime is called a "kernel" instead of a "runtime".

Ultimately I think what the author is getting at is a data problem, not a code problem. Or rather, it's yearning toward a world where data and code are strongly decoupled, conventions around data are standardized, so that processes written in disparate tooling can successfully interoperate locally. However I doubt there is much appetite for a "model of everything" registry (such things have been tried, and failed, in the past). That said we might take another stab at this, since LLMs make likely that software will become more dynamic in terms of translating data structures at runtime such that one program can examine a peer program and its data structures, and how to map them to local data structures, thus achieving interoperability without a centralized agreement on representation.