Why Vi(on) minimum values is higher than the typical value of PDTC124E (NPN transistor)?
Vi(on) value for the transistor is 2.5V and 1.7V are minimum and typical values respectively.

This is just a choice NXP made in representing the data. In this case you could also read the minimum value as the worst case value.

Since this specification point is "the minimum voltage you need to turn the transistor on while having Ic = 5 mA and having a Vce of 0.3 V".

As a designer what I need to know is: "What is the minimum (smallest) voltage that I would need to turn this transistor on under these conditions ?" That minimum is 2.5 V, as long as I apply 2.5 V or more (that is why 2.5 V is a minimum !) the transistor will be on.

In practice a typical transistor will only need 1.7 V but NXP will not guarantee that all these transistors behave in a "typical" way. So they specify that you need at least 2.5 V so that even the most stubborn transistor will turn on. NXP might test that they all work at 2.5 V and scrap the ones which do not turn on even at 2.5 V.