This clause is there in the PBO to give them legal cover in case they have to enforce it, but generally they don't. Generally the practice is to not charge extra price from customers who have already made full payment. They sometimes don't increase price for customers with partial payments as well or give them some time to make the balance payment according to booking price.
Charging updated price at the time of delivery from those who have already made full payment CAN happen, but is not the norm 
Given current increasing market competition, I don't think companies would want to get negative repute by doing this 