Given that these tribes are almost all, if not all, in Texas, they are not going to fare well. The Texans were extremely anti-Indian and were not big supporters of the Reservation concept. Just before the Civil War the government set up a reservation for the Comanche on the Brazos and then another in the Indian Territory. The Comanches wandered off the reservations at will and pillaged Texas settlements and ranches with impunity, until John R. Baylor led an expedition which severely chastised them and forced the government (in the form of Major George H. Thomas) to finally take action. If John R. Baylor or somebody like him ends up as Governor, you might well see an organized campaign to exterminate them, once and for all.
Indeed, differences over this issue, and the issue of cross-border raiding by Mexican bandits and revolutionaries, is the most likely reason why Texas just might leave the Confederacy. The "effete easterners" and their sympathy toward the Red Man were pretty much despised in Texas.
By the way, Baylor was the editor of an extremely anti-Indian newspaper called The White Man, and his brother listed his occupation on the 1860 Census as "Indian Killer." John, during the war, issued orders to have the Apaches invited in for peace talks...once there, the adults were to be plied with whiskey and then killed, and the children sold into slavery to defray the cost of the whiskey and bullets used to kill the adults. Not a very nice guy. And these were fairly typical Texans of the time, and both of them led active political lives. John was even elected to the Confederate Congress.