I feel like this is the main point of objection I have with this proposal. It doesn't have a mechanism to configure tools beyond passing them CLI arguments. It doesn't have a mechanism that allows authors to provide a library or API to end-users who might use these tools. This pushes the complexity outward to developers using these libraries, just like rpath and the like.
While we've been reassured that importing custom APIs into SwiftPM would be "easy", I'm not so sure... and therefore I think pushing this type of workflow out of the package and into the workspace proposal is a far better approach.