According to this source, it was by design.
http://www.tisanet.org/quarterly/3-2-4.pdf [page 8]
By the time Zheng’s authority surrendered to the Qing, the Qing unilaterally declared authority over Taiwan, but without actual administration. Indeed, the government had no intent to civilize the island. They simply wished to retain it as it was, uncultivated and primitive, because it was against the Qing’s interests to see a well-developed Taiwan that might cause a resurgence of anti-imperialism (Shepherd, 1993).
In 1874, an international conflict between the Qing and the Japan, which was caused by a Japanese shipwreck on the east coast, made the Qing change this policy and explore the mountainous area in order to comfort the indigenous peoples. However, faced with fiery resistance by indigenous tribes, the Qing never successfully extended its force into the mountainous aboriginal territory before Japan took over Taiwan in
1895 (Faure, 2001: 6, 26; Wolf, 1982).
On the eve of the Sino-Japanese War, about 45 percent of the island was governed by the Qing authority (mostly the western plains of the island), and the remaining
regions were under the control of various indigenous nations (Yosaburo, 1996:
212).
In 1874, Japan claimed that Taiwan was savage territory, not under the Qing’s
sovereignty, and as such could properly be claimed by whomever occupied it
(Harrison, 2001: 53).
Risking to steer this thread even further off-topic, here is a detailed account of the 1871 Mudan Village incident during which survivors of a Japanese shipwreck were killed by members of the Paiwan. The incident led to the invasion of Taiwan by Japan three years later.
I guess this is the US-Aborigines treaty, @hansioux is referring to:
As the Tokugawa regime was teetering on its last legs, U.S. consul to Amoy
(Xiamen) Charles LeGendre reprised, on a smaller scale, the 1853–54 U.S. missions to Tokyo in Langqiao, Taiwan. In the fall of 1867, LeGendre concluded a verbal agreement with the Langqiao headman Toketok to protect shipwrecked sailors from assault, robbery, and ransoming on Taiwan’s south coast.34 The agreement, like the 1854 Japan-U.S. treaty, reflected the efforts of maritime powers to make these as safer for greater volumes and velocities of commerce.
As a treaty-port consul in Xiamen, which subsumed Taiwan on the American
diplomatic organizational chart, LeGendre took the Langqiao Peninsula’s opacity
as a professional and personal affront. A letter to LeGendre from the Taiwan circuit attendant regarding the Rover referred to Articles 11 and 13 of the 1858 Treaty
of Tianjin to state “that whenever within the jurisdiction of the Emperor of China,
anyone shall molest Americans, the military and civil authorities must, on hearing of the same, try to punish the authors.” However, the note added—and this
became the sticking point for years to come—“the Savage country does not come
within the limits of our jurisdiction, and our military force is not able to operate
in it.”38 Finding this response unsatisfactory, LeGendre took the matter all the way
to the top (short of an imperial audience). In person, he proposed to the governorgeneral of Fujian and Zhejiang, Wu Tang, that the Langqiao Peninsula be occupied by Chinese inhabitants and garrisoned permanently by Qing forces.
A bit more about the Qing’s perspective (page 76 of that book)
The Qing’s inward orientation, as so many have noted, was not conducive to building national strength, as was made painfully clear when Li Hongzhang was left to fight Japan’s imperial forces with his regional navy in 1894. Its anachronistic and lowvelocity approach to diplomacy was best articulated in a formal response drafted by four members of the Zongli Yamen to pointed questions of Ōkubo Toshimichi at the September 14, 1874, negotiations for Japan’s withdrawal from Taiwan. The Qing ministers wrote:
In the aboriginal territory the Chinese Government let the indigenes keep their customs. Those who are able to pay tax pay it. Those who are talented enter nearby schools. We enforce generous and lenient policy to bring them up to a high level of edification. They are subject to the officials of the nearby districts. China stresses a gradual process of government, and has no intention to forcefully or too rapidly subjugate them. The natives of Hainan Island are treated the same. China has many regions of similar condition and every province has its own practices.
In other words, the Qing realm included many areas deserving of special treatment, depending on local conditions and levels of economic development. In some areas, it was appropriate to govern very little, if at all. Consequently, at the margins of Qing rule in Langqiao, LeGendre and then Saigō were forced to rely upon a collection of headmen, brokers, and guides for hire to locate allies in their search for the remains of fellow countrymen or in pursuit of malefactors who had killed them.