I don't want to make things more confusing than they potentially are, but just for the record, we are talking about different kinds of resources. The original poster was talking about the
Comfort and Barrett module (which is a great resource). This is not the same thing as what is available in the MSS tab. That is associated with the BibleWorks Manuscript Transcription Project which is BibleWorks' own baby.
So to try to answer your question. In Comfort and Barrett the red font for the underdot letters is a BibleWorks addition to help draw greater contrast between the underdot characters and the regular ones....
If you click on P1, you can see a papyrus that uses both black font no dots (characters that are clearly read from the papyrus), red font with underdots (characters that are present but not clear) and gray font bracketed (characters that would fit on the papyrus but are not extant).
The same kind of conventions were not followed in the BibleWorks Transcription project. In the BW transcription, characters only are in one color. I don't off the top of my head know of a verse that uses underdots, but they are possible. Gaps are not filled in if they exist in the text, so there are no gray bracketed texts in the transcriptions.