if it is going to take extra time to get catapults fitted then possibly one of the extra expenses might be the cost of keeping a lot of people employed in shipyards while waiting for the final bit of work to materialise
I think the extra time refers to the slip in F35C deliveries. Assuming that PoW was to be fitted first, most if not all of the flight deck steel units have yet to start fabrication. That means there would be time to modify the steel drawings etc prior to starting fabrication. The changes for EMALS do not materially affect the large lower block units for PoW which are the first ones in fabrication now, so they could proceed without delay. The only likely delays would be due to long-lead times for the energy storage flywheel systems, but that would not result in wholesale delays to the rest of the ship.
Not to say that wouldn't stop BAES claiming it would lead to such effects though! Short version is that unless the cost breakdown for the fit is published (a most unlikely event!), we'll never know. At the minute, we don't even know if the costs were fully contractor furnished or not. The conversion costing contract for QEC with the Naval Design Partnership was only let last October.....