I'm really sad that I lost my gist on this, but I was working on a system in Node.js for defining the capabilities of modules in an es module graph (as you suggest) where there might not be defined package boundaries. The implementation complexity (required changes to upstream V8) resulted in us going with node policies as they are today.

I don't remember the exact API, but basically an es module graph is a directed graph (e.g. edges have a direction), and because there is only one entrypoint in node, we can therefore create a hierarchy of modules. From this point on, you basically start at the root with X permissions, and from there each module can reduce the permissions of modules they import (or they can reduce their own permissions, but they can't raise them after that obviously).