So I'm not sure how other companies use this functionality but I can shed some light on our company.
We are moving to a single deliverable via axure that our on/off shore developers can work from. So for us, our developers would use the "redline" version while business would use the "business" version.
The "business" version would also be used to do things such as usability testing with our users which is why we don't need to show redlines, annotations, etc within the business link.
However for the redline version, it would be helpful to keep all of the information for an element/object within the black panel of the redline tool. This would help support our offshore developers who work odd hours by providing all the information that they need about an object/element in one place and within context of the other available information.
I could see how the information within the black panel would start to get very long- perhaps adding an expand/collapse within the black panel for the notes would be a good way to approach it.
Please see below: