I do not understand. The c.t. maximum output voltage is not 1 V. In that circuit with those component values, it is approx 1.6 V rms. You will get that with 100 A rms flowing in the c.t. primary circuit.
Are you saying that your maximum current will be less than 100 A, therefore you need to increase the sensitivity of the input so that the Arduino input is 1.6 V (≈ 4.5 V peak to peak, to allow for component tolerances) at a lower current?
If yes, then you increase the value of the burden resistor (33 Ω). The maths are explained in the article, you must calculate the resistance that gives you approximately 1.6 V at the maximum current you want to measure, and remember the c.t. gives you 50 mA out for 100 A in the main cable.