At the moment, you can specify colors for some elements and not some others. In most cases this is fine as I use mostly black/grey only wireframes to keep a streamlined look, but I tend to resort to annotations relatively often to provide additional information.
"Callout" and "scratch out" features both support color customization, but the "note" annotation doesn't.
I don't know the complexity for this change request in your code, but I think maybe other people would like to see this evolve as well, maybe to use color-coded annotations for different uses (for instance, yellow or blue for informational notes, red for notes about error handling, grey for actions, or anything else).
Just a thought.
