They are tracked separately as opposed to stacking for a total effective level. There is nothing prohibiting you from making the same creature both an animal companion and a wild cohort. It's just specifying that you use the Wild Cohort chart for the Wild Cohort benefits, and you use the Animal Companion chart for the Animal Companion benefits, and that they are independent of each other and not the same ability.

You can dismiss your wild cohort and gain another one. You can dismiss your animal companion and gain another one. You can dismiss both and gain one creature to fill the role of both your animal companion and your wild cohort, provided that creature can fit within the restrictions of both.