Wrt. points 1 and 2: One solution I imagine could work quite nicely here, and would be nice even without this particular motivation, would be to compose with the upcoming script support and allow manifests to declare build-dependencies together with the import stanzas.
This would, I think, lead to a model that is quite understandable to the user, and apart from allowing type-safe configuration for build plugins it could allow common patterns seen in package files to be pulled into libraries.
This is, of course, a feature a little bigger than something focused on just build plugin config, but it's such a natural composition of features I think I quite like the idea.