Actually, having more 4 car units is what really brings versatility. Think of the service pattern after 9/11. Such would be impossible with the original R179 configuration. With the new configuration, one could just take the C's R179s and put them on the J and M, while anything could be placed on the C to backfill. Furthermore, since the eastern division is one of the fastest growing parts of the system, it is essential that there be more cars available for the eastern division than are currently assigned. Look at recent history- the growth of the eastern division has outpaced the new cars built for it on 4 occasions in the last 15 years! (R143, R160A Base, R160A Option 2, and the original R179 configuration)
On a per car basis, yes, but it results in a cheaper per train cost, as well as a lower overall cost.