This is because, initially, the Nara Line was built by Nara Railways between Kyoto Station and Nara Station, but Kizu Station and other stations south of Kizu Station were separated from the Nara Line in order to be part of a route between Osaka and Nagoya after Nara Railways was merged into Kansai Railways.
これは当初奈良鉄道によって京都～奈良間が建設されたものの、関西鉄道に合併された後に大阪～名古屋ルートの一部として木津以南を分離された、との経緯による。