That is true but when you get to the point of deleting bits of kit from the cost-per-hour estimates then the customers are going to get nervous. It was these very same bits of kit that made the aircraft competitive and to adjust in this way smacks of spin. I'm sure if I deleted all the features the F-16 has over the Hawk from the costs-per-hour I could make it look pretty cheap too.
It is unwise to split-out the cost of the EOTS just because podded systems are costed separately on 'legacy' jets. Removing, repairing, modifying or upgrading a pod is relatively easy and does not necessarily ground a legacy aircraft; as an embedded and integrated system upgrading EOTS will not be as easy. If, as seems likely, the USMC add a pod in addition to the EOTS then the costs for both will have to be shown on balance sheet somewhere.