The title sums it up. The first two pieces of territory that eventually made up "Hong Kong" of today mainly Hong Kong Island and the Kowloon Peninsula were deeded to the U.K. long before the New Territories. Why were they then subsequently included with the New Territories in the 99 year lease agreement?
There were 2 reasons for the U.K decided to handover all three territories to China. The first reason was China and the U.K had different opinions on Hong Kong status. The second one is related to the infrastructure of Hong Kong.
As we all know, the British colony's status was based on three treaties. Which were "Treaty of Nanking"(1842), "Convention of Peking"(1860), and "The Second Convention of Peking"(1898). According to these 3 treaties, Hong Kong Island and the Kowloon Peninsula ceded to the U.K. However, the Chinese government did not recognize these 3 treaties. The Chinese viewed the treaties as unequal treaties. They suggested that the Qing government was forced to sign them so the treaties did not possess any legitimacy. While the Chinese government treated them as nothing, the 3 treaties unable to become a bargaining chip.
Another reason is the infrastructure of Hong Kong cannot be separated. Though Hong Kong can be divided into 3 sections which are Hong Kong Island, the Kowloon Peninsula, and the New territories. However, the colony government never independently develop the 3 sections. It's meaningless to control Hong Kong Island and Kowloon without N.T. and vice versa. So it is impractical to return N.T. and keep the remaining parts.
Sources
John M.Carroll, "A Concise History of Hong Kong", Rowman & Littlefield Publishers, Inc., UK, 2007
Steve Tsang, "A Modern History of Hong Kong", I.B.Tauris & Co. Ltd., 2004
徐承恩: "城邦舊事"，青森文化，2016年3月
彭定康(Chris Patten ): "東方與西方: 彭定康治港經驗"(East and West: The Last Governor of Hong Kong on Power Freedom and the Future)，時報出版社，1998年10月