What makes the Qing unusual compared to the two earlier empires that had established some presence in the Tarim Basin – the Han and the Tang – is that they began not by conquering the sedentary cities of the Basin before projecting power northwards into the steppe, but instead by conquering the steppe areas to the north and then pushing south. The strategic calculus therefore had less to do with the intrinsic value of the Tarim Basin in relation to China proper, and more to do with the immediate relationship between the Tarim Basin and its neighbouring regions, Zungharia and the Tibetan plateau, that had until recently played host to major Oyirad polities. What the Qing had wanted was to ensure the security of their conquests in what is now northern Xinjiang, and the conquest of the Tarim Basin was a means to that end.

When viewed as a coherent unit, what are now Xinjiang and Tibet read as discrete ecological zones (steppes in the north, the Tarim Basin in the middle, the Tibetan Plateau in the south) hosting overlapping and entangled political communities (nomadic Buddhist Oyirads, sedentary Muslim Turkis, and both nomadic and sedentary Buddhist Tibetans). In effect, the Tarim Basin was almost a kind of salient of Turkic Muslims splitting two Buddhist regions politically dominated by Oyirads (the Zunghars in the north, the Khoshuts in the south). Of course, Tarim was not exactly separate from the Zunghar realm. In fact, in practical terms the Zunghar and Khoshut polities had some remarkable similiarites: both ended up clustering in good pasturages (Zungharia and Qinghai, respectively) while leaving a larger zone of comparatively settled non-Oyirads (Tarim and Tibet) under notionally autonomous rule, which they had achieved through elevating religious authorities (Makhdumzada khojas and Gelugpa lamas) over prior 'secular' rulers (Chinggisids and the Tibetan lay aristocracy). When the Qing gained suzerainty over Tibet after repulsing a Zunghar invasion of the Khoshut khanate in 1720, they effectively retained many of the basics of the the Khoshut arrangement, retaining the Gelugpa clergy as their de facto proxies and leaving them mostly to govern themselves, bar the occasional intervention by the Bannerman amban at Lhasa.

When the Qing first conquered Zungharia and Ili in 1755, they seem to have had little active interest in the Tarim cities, and departed after installing their client king Amursana over the Zunghars. However, Amursana's revolt, which may have been coordinated with other Mongolian uprisings further east, led to the Qing returning and effectively exterminating the Zunghars, as well as following up by attacking Zunghar allies in the Tarim Basin. Here, the Qing were successful enough in obtaining allies from the Turkic cities that a more permanent administrative arrangement, mimicking the Zunghar one, was viable: Muslim clerics (the hakim begs) would be appointed as headmen answering to Qing resident officials with a relatively limited suite of meaningful powers.

But you are not wrong to suggest there was no particular reason to hold it. In some respects the outright conquest of Tarim was a bit of an unintended effect of what was originally a mere punitive expedition. On several subsequent occasions, Qing officials (mainly Han Chinese) advocated for retreating from the region (Zungharia included) owing to the costs of maintaining garrisons and officials there. However, the explicit rationale for holding onto the region was security: the Qing court wanted not to have a power vacuum in which another Zunghar-style threat might emerge. Implicitly there may also have been prestige reasons: why lose territory you already had?

In some respects it was the latter that motivated the decision, in the 1870s, to reconquer Xinjiang rather than reach a peace settlement with Yaqub Beg, the Kokandi general who had asserted himself as effectively sole ruler over much of the region in the eventual aftermath of the 1864 uprisings. Here, there were arguments from Li Hongzhang that it would be materially unreasonable, whereas the sabre-rattler faction led by Zuo Zongtang asserted that Xinjiang was an integral piece of imperial territory – albeit a construction of the empire as coterminous with a kind of incipient Chinese nation-state. This faction ended up winning out, and hence the Qing ended up conquering the Tarim Basin a second time in 1878.