Not an answer to OP, but to those who need annotation. I’ve made a hypothes.is plugin.
Until a native clipper comes up, I may add embedding for a webpage with hypothes.is on the left in an iframe. Problem is, most pages does not want to be rendered in iframes, due to clickjacking. I can redirect those pages to the hypothes.is via proxy. I will try to emulate PDF workflow, let me see whether it is possible.