How can we use the same charge-pumps circuit for varying input voltage?
The block diagrams are often, at the same time, difficult to interpret, and oversimplifying things. It is often worth reading datasheets text entirely.

In this specific case, see at the bottom of page 13:


  Pump Regulator
  
  The gate drivers are powered by a programmable voltage internal
  regulator which limits the supply to the drivers and therefore
  the maximum gate voltage.


There, you have your answer: the charge pump multiplies the input voltage by a fixed integer number, but it is followed by a regulator that clamps this voltage so the gate voltage is not excessive.