I've never really tried to delve into the Union (army) signal flags, and precious few of any seem to have served, from either side. Nothing especially attractive about them -- probably became cleaning rags. Only those who understood their story cherished them. (I AM on a quest for a first generation sectional flag pole for photos or description for study.)
The dark(est) flag of the set is variously noted as black, blue, dark blue, but always with white center square. I've seen only the requisitions, pictures, and descriptions. Black seems not to have survived the sun exposure as well as the "navy blue," so perhaps something about the dyes involved. Within one CS signal outfit, there is some evidence that the "blue" flag was reserved for unofficial "chatter" among stations, otherwise the choice of red or white (with opposite-color centers) for official messages, depending on background. If the black was intended for snow, I'd imagine less need in the South, plus adequacy of red flag for the job. Noted one report of "brown" being used by CS sig officer organizing a group for defense of Atlanta.
Fully agree with you on "Colours of the Gray," Rebecca Rose's magnum opus before going to Va Hist Soc. I'm awaiting the Biggs work some day, now that Howie is no longer with us.