More likely it has to do with iOS 9 than anything else.
A user in the JB forums just went back to using his iPhone 6 because his new 6s is in an unbootable state after restoring iOS 9.
Apple replaced my iPhone 6+ last Sunday for the price of a screen repair because restoring to iOS 9 caused a bootloop. The Apple genius told me that Apple is having a lot of issues with iOS 9 and restores right now.
I don't think iOS 9 was really ready yet.
Just curious, but shouldn't this have been covered under warranty rather than you paying extra? Unless the screen was damaged beforehand?