"Total War" is a bit grandiose and ambitious, but as far as I know very few Native American or American Indian groups in the USA had any sort of rules against harming noncombatants in war.
As far as I know, as a general rule Native Americans or American Indians in the USA didn't have any sort of social rules against killing noncombatants. So they sometimes killed women and children when they had opportunities to, and sometimes captured them for various purposes - such as later torturing them to death, or mass rape, or selling them as slaves, or adopting them and making them parts of their families and tribes.
EASTERN WOODLAND GROUPS
American colonists and later American citizens recorded many examples of eastern woodlands tribes attacking isolated farms and settlements and either killing white women and children instantly, or taking them away to be later tortured to death, or raped, or enslaved and maybe sold for profit, or maybe ransomed by relatives, or maybe adopted and made part of the community and transformed into members of the tribe.
And some people might suppose that maybe the eastern woodlands tribes hated whites much more than they hated members of other tribes, and that they would not treat women and children of other eastern woodlands tribes as harshly as they treated white women and children.
In the rather genocidal Beaver Wars of 1629-1701 the Iroquois Confederation sought to control the trade in beaver furs with Europeans, and more or less made itself the overlord of most of the tribes in a vast area in what later became the northeastern USA and southeastern Canada.
Many enemies of the Iroquois were totally destroyed during the Beaver Wars.
The wars were brutal and are considered one of the bloodiest series of conflicts in the history of North America. As the Iroquois effectively destroyed several large tribal confederacies—including the Mahican, Huron, Neutral, Erie, Susquehannock and northern Algonquins. They became dominant in the region and enlarged their territory, realigning the tribal geography of North America. The Iroquois gained control of the New England frontier and Ohio River valley lands as hunting ground, from about 1670 onward.
After the Iroquois destroyed an enemy nation, the former members of it would be reduced to three different types.
1) Iroquois captives who would be gradually assimilated and turned into Iroquois. In many Iroquois villages the majority of the population consisted of assimilated former members of enemy nations.
2) Fugitives who would seek shelter with other tribes and nations and gradually assimilate into them.
3) Rotting corpses — and possibly ashes in the cases of any burned to death.
In some cases Iroquois brutality might have been revenge for brutal attacks by their neighbors in previous wars. But I doubt that was the case when the Iroquois destroyed the Neutral Nation.
Therefore, I guess that the many eastern woodlands tribes sometimes treated the women, children, old people,and other noncombatants of enemy tribes with the same brutality they were sometimes recorded by whites as using against white noncombatants.
WESTERN NATIONS, TRIBES, AND GROUPS
In the western part of the USA the situation was basically the same, with one exception. Most of the eastern woodlands tribes had warrior cultures where men were expected to fight enemy tribes from time to time.
The western two thirds of the USA has very varied climates, and there are hundreds of different nations, tribes, and groups who lived there during times when their actions were written about by Europeans, who had and have many different cultures. Many of those tribes migrated from other regions only a few centuries ago, as part of the constant migrations, splitting up, and merging of various peoples that has been going on since the dawn of humanity.
Many of those groups in the trans Mississippi West had non aggressive cultures and their members wouldn't attack anyone who wasn't bothering them, though they would defend themselves against attacks and might strike back to retaliate and to deter future attacks.
Of course the most famous nations and tribes in the West had warrior cultures, where men were expected to not only defend their groups but also to attack other tribes and steal and kill to make their reputations. So the famous plains warrior tribes and the Navajos and Apaches, etc., etc., tended to be at war with all of their neighbors - except for any allies they had - more or less constantly.
And as far as I know, almost no groups in the trans-Mississippi West, whether non aggressive or warriors, had any rules against harming noncombatants.
Except that when the Modoc War started with a brief gunfight in the camp of the non reservation Modocs on November 28, 1872, Captain Jackson retreated with his troops and the Modocs under Captain Jack fled, eventually taking refuge in the lava beds. A band of Modocs under Hooker Jim killed 18 settlers on November 29 and 30. As far as I remember, the warriors in those raids killed only men and spared women and children, though the youngest "man" they killed was only eleven.
And a bigger exception was the non treaty band of Nez Perce in the Nez Perce War of 1877. As far as I remember, the Nez Perce warriors committed almost no atrocities or war crimes during that bloody conflict.
As far as I remember, those are the exceptions that prove the rule.
Sacred Ridge Massacre. At the Sacred Ridge archaeological site southwest of Durango, Colorado, bones of about 35 persons were found in the 21st century showing signs of torture and mutilation by their enemies. The date of the massacre should have been roughly about 803 to 810.
At the Crow Creek Site, South Dakota, archaeologists have found the remains of at least 486 person, men, women, and children, of an unidentified group who were killed by members of an unidentified group and whose bodies were eventually buried by someone - in the unfinished defensive ditch around the village. The Crow Creek massacre happened in the mid 1300s.
In 1694, Apaches brought a large number of captive children to the trading fair in New Mexico, but for some reason there were not enough buyers, so the Apaches beheaded all their slaves in full view of the Spaniards.
The Skidi Pawnees in Village Across a Hill practiced human sacrifice in their annual Morning Star ritual, sacrificing a captured girl, when they were first contacted by whites, but reformers began to urge that the sacrifices stop. In 1817 Petalesharo rescued a Comanche girl from sacrifice.
The last known sacrifice was of Haxti, a 14 year-old Oglala Lakota girl, on 22 April 1838.
The French responded by sending Bourgmont to make peace (in the French interest) between the Pawnees and their enemies in 1724. He reported that the Pawnee were a strong tribe and good horsemen, but, located at the far end of every trade route for European goods, were unfamiliar with Europeans and were treated like country bumpkins by their southern relatives. The mutual hatred between Pawnees and Apaches was so great that both sides were cooking and eating many of their captives.5:47 Bourgmont's "peace" had little effect.
In 1871, Pinal and Aravaipa Apaches lead by Eskiminzin made peace and settled down near Camp Grant, Arizona. But some people, suspecting they were still secretly raiding, or for other reasons, weren't happy. William S. Ouray and Jesus Maria Elias formed a Committee of Public Safety in Tuscon and got Francisco Galerita, leader of the Tohono O'odham at San Xavier, to join them.
On April 30, 1871, 6 Anglo Americas, 48 Hispanic Americans, and 92 Tohono O'odham attacked the sleeping Apache camp and killed about 144 Apaches - 8 men, the rest women and children. 29 Apache children were captured and sold into slavery, despite slavery being illegal in both the USA and Mexico.
Despite being of different cultures and races, the various groups could all agree that the only good Apache was a dead Apache.
On one such raid, 5 August 1873, a Sioux war party of over 1,000 warriors ambushed a Pawnee hunting party of 350 men, women, and children. The Pawnee had gained permission to leave the reservation and hunt buffalo. About 70 Pawnee were killed in this attack, which occurred in a canyon in present-day Hitchcock County. The site is known as Massacre Canyon.
In the Dull Knife Fight or Battle on the Red Fork, 25 November 1876, Colonel Mackenzie's force of US cavalry and hundreds of Indian scouts of the Pawnee, Shoshone, Bannock, Arapaho, Sioux, and Cheyenne tribes defeated and destroyed the main winter camp of the Northern Cheyenne. As I remember, among the loot found in the camp was a sack containing a number of hands of Shoshone babies acquired in a recent fight.
And these are some examples I could remember and/or look up of Native Americans or American Indians committing war crimes and atrocities against other American Indians.