New York City has 5 boroughs. Manhattan is one of the 2 smallest boroughs. But every weekday morning, when people bus/drive/ride into work from other cities/states, Manhattans population swells to almost 3 times.
Peshawar is similar to Manhattan in concept. Lahore and Karachi are not as similar, because people tend to come in to settle in Lahore and Karachi, hence, most of the workers tend to become residents of the city. Peshawar has tons of commuters coming in and going out on a daily basis from across various areas of KPK. That translates into a higher ridership for natural reasons. Also add to that the fact that Peshawars metro route runs through denser areas with fewer people having cars or personal conveyance. In Lahore, ferozpur road is routinely choked up below, while the metro breezes above with an average 50% occupancy (Its interesting that whenever Punjab govt quotes metro figures, they quote the capacity of 130,000, not the ridership, which is far less).
It remains to be seen whether Peshawar can achieve the 480,000 ridership 'target', but its a matter of common sense that it would be higher than Lahore, because of obvious factors.