I don't think this will help either...
But FWIW Kovid Goyal has had annotations on his TODO list for calibre for a while.
At the moment he is massively busy rewriting the content server, though I have hopes that the server rewrite will pave the way for a native browser reader, which in turn requires revamping the ebook-viewer (once you're there anyway...).
Just you wait, it will support annotations/bookmarking one of these days!