The element annotation tool allows for annotating referenced elements, but only if you select to have all elements annotated. This seems like a major flaw in the process. Since there could be multiple references with multiple elements, having to select all elements in order to annotate referenced elements means the program has to process all elements, which can take a long time. It'd be better if we could graphically select the elements we want annotated, whether they are drawn in or referenced in.
I've also run into an issue where I'm annotating an element using a text favorite that displays an item property attached to the element. When I use the element annotation and the element is a referenced element, it does not find the item property. It will only display the item property when the element is drawn into the file. My workflow would be a lot simpler if this worked properly.