Because of the serious nature of Kaliyan and the boons claimed by him. So the power of the 'Supreme Ekam' was given birth as son of Lord Narayana in the Name of Vaikundar. Hence Vaikundar is not only a unique avatar but also the only able power to destroy the evil Kali.
Vaikundar arose as the son of Lord Narayana from the power of the 'Supreme Ekam' because of the gravity of Kaliyan's circumstances and the benefits he offered. This makes Vaikundar not only a singular avatar but also the sole authority that can overcome the malevolent Kali.