At some point (pre-Civil War) the US gave up on the idea of there being permanent Indian Lands. It was expected that the tribes would essentially disappear and the US Govt's actions were influenced by that belief (in my opinion) and much has been done to try to facilitate that, like the relocation programs of the 1950s. The Five Civilized Tribes, as "domestic dependent nations" posed a challenge because the US Supreme Court kept ruling that the US Govt had to follow the 'rule of law' in its dealings with them.
The surveys for wagon roads and railroads across Indian Territory began before the war, showing the US Govt planned on putting them there regardless of oppostion from the tribes. They were required in the Treaties of 1866 and huge right-of-ways and sidings were given to the railroads.
Competition between the railroads and the Texas cattlemen fit with the US desire to 'legally' acquire more Indian land. The railroads and white settlers won. The tribes and the cattlemen lost. Congress ruled that the Tribes could not lease land to Texas cattlemen because commerce with the tribes was restricted to Congress (an interesting interpretation which changes to suit the situation). The leases paid for schools and infrastructure of the tribes. The leases allowed the cattlemen to drive their cattle into the Indian Territory to graze and then drive them to Kansas markets. The railroads wanted to transport the cattle. The settlers wanted the land. The tribes had to sell their land to the US government to pay for their infrastructure and the US opened the land for settlement. The cattlemen couldn't drive and graze their cattle so they had to send them to Kansas by rail. As they say, "It's all about the Benjamins". It resulted in a "redistribution of wealth" and economically hurt the tribal governments. The attempt to create the State of Sequoyah was too late, the land was allotted, and Oklahoma became a state. Everyone thought the Five Civilized Tribes were gone but the US Supreme Court ruled that people, not land, make a nation ("a body politic") and the tribes reestablished their governments, became federally recognized by the Bureau of Indian Affairs, and have grown to what they are today.