This is a bit of a "yes, but" answer. Yes, the Mississippian civilization, like many Native American civilizations, included wars of conquest and tributary relationships. This was pretty standard for Native America: the Jamestown settlers, for instance, landed in the region of the Powhatan Confederacy. This was effectively an empire, wherein Powhatan commanded a network of tributary relationships and exercised partial control over a vast swathe of land. Pekka Hämäläinen has done some amazing scholarship on the Comanche Empire, and has argued Lakota power formations should also be understood as empires. I highly recommend checking out Hämäläinen's and/or Mississippian scholarship, because it's quite interesting.

This is all to say that the framing of Native nations as akin to empires is not, in itself, incorrect. This article, however, is not interested in Indigenous power formations. It is essentially taking the age-old (seriously, it's been around since the 1400s) argument that the brutality of some Native people justifies the brutality of Europeans in their genocidal campaign against Native Americans. The author wants us to accept the premise that European conquest of North America was the same as Native conquest.

This premise is incorrect. The conquest of North America was distinct from anything the continent had seen before. Native empires generally relied on tributary relationships-- that is, a portion of agricultural yield, game, crafts, or other valuables of conquered Native groups would be offered to the leader of the empire. Crucially, though, conquered groups were usually allowed to maintain their land and culture. Their obligation as part of the empire was to furnish material support, rather than disappear. This wasn't always the case--the Comanche Empire especially often displaced Native people from their traditional land-- but it was a general pattern.

By contrast, European conquest of North America was settler-colonial in nature. There's a lot of settler-colonial theory out there, but in short, it is a form of colonialism in which a settler population seeks to replace the Indigenous population of a land through elimination-- effectively, genocide. Europeans didn't want simple tribute from Native nations; they wanted their land. This required varying forms of genocide, from outright massacre to cultural genocide to abduction of children. The settler-colonial conquest of America was an effort at total elimination of Native lifeways and claims to land. It was unsuccessful, of course: Native nations have, against all odds, survived, maintained their cultures, and fought hard to secure some amount of land. But it was a uniquely totalizing form of colonialism that sought a complete replacement of Native people, cultures and land with settler populations.

In sum: Native power formations might be considered empires, but that doesn't mean their forms of conquest parallel the settler-colonial project in North America. Happy to answer Qs/ provide sources if you want.

Quick footnote: the author of this article also argues that, because nonwhite people exist in the U.S., settler-colonialism doesn't work somehow. But of course, nonwhite people can be settlers. For one great historical account of Black participation in settler-colonial expansion, see Kendra Fields' Growing Up with the Country.

EDIT: Additional info, as requested by mods. Let's do a bit of a case study in the Lakota Sioux power formation-- I'll call it an empire, but understand there's debate to be had about the utility of that term. The Lakota entered their traditional territory (present-day Dakotas, Montana, Nebraska and Wyoming) from the east in the late 18th century, splintering from the Dakota Sioux. Driven by a desire to hunt bison, the Lakota group's desired land base was already occupied by nomadic hunter groups (Kiowas, Cheyennes, Arapaho) and sedentary farming groups (Mandans, Hidatsas, Arikara). On horseback, and toting guns, the Lakota conquered its way westward; as Hämäläinen describes, this was not a unified push but rather "...a sum of countless little invasions— autonomous bands inching their way westward, reacting to changing local circumstances rather than any overarching political agenda" (45). These instances of conquest were decentralized, but by the 19th century the Lakota empire was established in the western interior, with Cheyenne and Arapaho allies. It continued to dominate the region by engaging in resource exploitation; for example, horses paid as tribute or captured in raids were sold to the U.S. for guns. Hämäläinen identifies Arikaras as a particularly good example of the imperial might of the Lakota; they "...were reduced to tributary vassals who supplied Lakotas with corn and bought their meat and hides for greatly inflated prices" (48).

Every Native power formation was distinct, but hopefully this provides an idea of what a Native empire may have looked like. Oppressive, asymmetrical power dynamics and the usurping of control over land via co-optation of hunting rights and tributary relationships-- but still distinct from the genocidal conquest of Native nations by Europeans.

Source (and I recommend the whole piece for a great overview of Comanche, Lakota, and Iroquois empires): Pekka Hämäläinen, "The Shapes of Power: Indians, Europeans, and North American Worlds from the Seventeenth to the Nineteenth Century" in Contested Spaces of Early America, edited by Barr & Countryman.