Thank you for re-opening this. The second document shows we need some non-trivial fixes. We're mapping, note, annotation and notes to <div>. However, as your document shows, these can occur within a <p/> and contain their own <p/>. We'll want to avoid putting a <p/> inside a <div/> and a <p/> inside a <p/>.
<p>text<div><p>this is an annotation</p></div></p>.
Should we map note, annotation and notes to <span/> instead of <div/>? Or, should we close the <p> when we hit an annotation and friends?