In the compiled service records, Maj. Broke Arm is shown as an officer in Col. R.W. Lee's command on N.W. frontier of Indian Territory. On May 28, 1863, he received powder, lead, musket caps, rifle caps, musket flints, and rifle flints at Camp Davis, approved by Brig Gen D.H. Cooper. This would seems to suggest his men were armed with a mixture of flintlock and percussion muskets and rifles.
Captain George Washington is also shown as an officer in R.W. Lee's command. (I know almost nothing about R.W. Lee other than he was, early on, a lieutenant and acting adjutant in the 1st Choctaw & Chickasaw Mtd Rifles -- Cooper's Regiment).
There is a reference to Maj Broke Arm's command in, if I recall correctly, "Cherokee Cavaliers" in a letter to or from Augustus Chouteau that states they are at the Wichita Agency -- don't hold me to that! I'll look it up again and post on the board.
Based on my limited knowledge on the subject and scant records, it is my opinion that it is unlikely a company of Comanche served as "Confederate troops" but may have been occassionally supplied and, as was common, given presents by Confederates or even by Watie. I presume their activities were a continuation of a lifestyle/culture of raiding for plunder, the only difference being they agreed to direct their raids on Kansas and on traffic on the Santa Fe Trail and not on Texans or Chickasaw or others allied with the Confederacy.
A point I was trying to express earlier is that these are not typical Indians in the Civil War. I'm a little concerned that portrayal of a Comanche as a Confederate Indian perpetuates the stereotype that all Indians are like Plains Indians. At the same time, if it sparks someone's interest to study more for themselves, great! Your original post mentioned portrayal of a Native persona of a trans-miss Confederate which immediately made me think of the primary Indian units that were enrolled, armed and supplied (poorly), and under direct military authority of the Confederate military command structure.
I would not be surprised to find one or a few individuals from any tribe or nationality in any unit. Thomas Anderson was a Scandinavian emigrant serving as Watie's adjutant. There were some Cherokee, Caddo, and Shawnee (and undoubted others) living in the Chickasaw Nation before the war. It would be plausable that there was one or a few Comanche serving in the "typical" Confederate Indian regiments but my guess would be they would be dressed more like their fellow soldiers than the garb we associate with the Plains Tribes during the period.
Okay -- enough about stuff I know nothing about! ;-) I'll post anything else I run across and you please do the same.
If you aren't familiar with Annie Abel's three volumes on the American Indian in the Civil War, you may want to look into them. I believe their full text is available online.
Thanks,
Ken