@cdweeks glad your loving Reftagger! I can understand that must be a tedious. Unfortunately we are not adding new features at this time. I will pass along the suggestion though. Also feel free to submit your request at https://feedback.faithlife.com/boards/faithlife-reftagger.
We don’t currently support customizing font color. That said looking at the behavior this seems more like a bug as it’s inconsistent. I’ve submitted a case to investigate more.