The tribal territories were independent. They're even described as independent at the time. In fact it was more than only the tribal territories that were independent. Here is a quote from Record of Frontier Expeditions
3. The Country of the Independent Tribes. - Turning to the mountainous region between the settled districts and Afghanistan, to the extreme north lies the agency of Dir, Swat and Chitral. Chitral itself consists of a narrow valley enclosed between rugged mountains. Below Chitral are found the thickly timbered forests of Dir and Bajour, and the fertile y valles of the Panjkora and Swat rivers. Between this agency and the Khyber Pass lie the Mohmand hills, a rough country with but little cultivation, under the political control of Peshawar. West and south-west of the Khyber again is the country of the Afridis and the Orakzais. The boundary of the province here follows the line of the Safed Koh, which overlooks the Afridi Tirah and the upper Kurram valley. Dotted with towered hamlets and stately chinas groves the valley of the Kurram runs south-east from the Peiwar Kotal (below the great peak of Sikaram), past Thal in the Miranzai valley, through the southern Kohat hills to Bannu. South of the Kurram is the Tochi valley, separating it from Waziristan, an isolated mountainous district bounded on the south by the Gomal and the gorges that lead to the Wana plain. The lower ridges of the frontier mountain system are usually bare and treeless, but here and there, as in the Kaitu valley, in northern Waziristan and round Kaniguram in the south, are forest clad and enclose narrow but fertile and well-irrigated dales. In places, too, as, for instance, round Shawal, the summer grazing ground of the Darwesh Khel Waziris, aria on the slopes of Pir Ghol, there is good pasturage and a fair sprinkling of deodars. The valleys of the Tochi and Wana are both fertile, but are very different in character. The former is a long narrow valley, with a rich fringe of cultivation bordering the river; the latter is a wide open alluvial plain, cultivated only on one side, and for the rest rough stony waste. South of the Gomal the Suliman Range culminates in the famous Takht-iSuliman in the Largha Sherani country, a political dependency of Dera Ismail Khan district. The Kaisargarh peak of the Takht-iSuliman is II,300 ft. above sea-level.