>doesn't the free-form nature of the "body" part of these configuration files lead to an inevitably unverifiable process?

The non-deterministic statistical nature of LLMs means it's inherently an "inevitably unverifiable process" to begin with, even if you pass it some type-checked, linted, skills file or prompt format.

Besides, YAML or JSON or XML or free-form text, for the LLM it's just tokens.

At best you could parse the more structured docs with external tools more easily, but that's about it, not much difference when it comes to their LLM consumption.