Semantic web uses IRIs in triples. They serve as identifiers, not locators (URL). This is because semantic web talks about more than just files.
The Web Annotation spec talks about web resources which should be dereferencable. That is a naive assumption that makes the approach brittle. But one can annotate 'sourceDate' and 'cached' which indicate the date for the annotated version and a location for a copy.
When you're annotation a resource it's best to also store a copy. The Web Annotations specification allows this.
Do you know if there's any precedent re: people getting upset about that copy? If I annotate an article that was originally served with ads, or behind a paywall, I'll probably not include that stuff in my copy. If people then start linking to my copy instead of the original, I could imagine that feathers would be ruffled.
But otherwise yes. I'll have to give that a closer look and use as much of it as I can.