Your point that the only article I know of for these flags is in the MC&H shows that more work needs to be done along these lines.
The small First National flags with the four-pointed stars were made as lance pennants for the several lancer cavalry units raised earlier in the war. I have copies of the contracts from Laura Lacy, Burger & Brother and Hetty Cary for making these flags. They might have been pressed into use as guide flags when the lancer units did not pan out. Lancer units, historically, always use variations of their national colors on a smaller scale for their lances.
There is a guide flag in private hands for either an Alabama regiment or NC regiment that is a single color with the digit in the center (a 4 I think).