I don't have background other than reading the background included in the decision, but it seems that in late 1800s/early 1900s, the land was allotted into parcels with individual ownership by members of the Creek Nation, and after a time that ownership became freely conveyable to any person.

Conveying property to a non-member does not remove land from a reservation, and this ruling does not void any conveyances. Whoever owns the land, owns the land. This ruling just makes it clear that all of the land within the treaty boundaries is still a reservation. I don't know all of the implications this will have, but I imagine a lot of things done by the state of Oklahoma assuming they were operating within the state of Oklahoma may need to be reviewed, given that they were operating within the Creek Nation.

For example, can the state allow formation of counties and cities within the Creek Nation? What about if said counties and cities were formed inclusive of only land owned by non-members of the Creek Nation?

Of course, the court mentioned that Congress is free to stop honoring the treaty, the only requirement is that it must do it explicitly.