If you have to spend more on a component of a device that you won’t be increasing the price tag of, disabling the core for a lower model ensures the cost staying the same. There isn’t any savings Apple is pocketing while the customer paying the same price tag.
I am pretty sure Apple pays per wafer, not per each individual chips. Apple will be able to save money by being able to harvest more chips per wafer with the ability to use 4-core GPU variants instead of just 5-core ones. There could be some chips that works well with 4 cores but doesn't work up to the intended performance with 5 for example.