Difficult question to answer because there are so many variables.
What is the author (Tony Capaccio) and his sources definition of the configuration of the FORD, KENNEDY and ENTERPRISE in the context of the $40B? What year inflation adjusted dollars are being used? Is it sail away cost, acquisition cost, life cycle cost or total ownership cost...or a hybrid? There are multiple contracts let by the three major DON SYSCOMS to outfit a carrier. Are there any substantially new technologies involved (I'd say yes with a plural)? Where are they on the learning curve (technique to explain why building more than one of something costs less each iteration, all other things being equal).
What is the author's reputation, background and "beat"?
Who is being quoted and what might their motivations be, and what are their yard sticks?
Who is not being quoted and why?
What are some of the most notable technology developments to learn from:
- We have gone from straight decks to angle decks
- No catapults to hydraulic cats, to steam cats and now EMALS
- Cable launch to tow bar launch
- petroleum burners to nuclear reactors for propulsion
- 8 reactors (it was an experiment one time) to 2 reactors per carrier
All of the above and many more advancements required significant one time R&D expenditures to mature the technologies to a high enough level for deployment, and yes there are trades done.
America's carrier aviation capability represents a significant contribution to America's total combat effectiveness when you compare it total combat effectiveness without carrier aviation. Even small increases in combat effectiveness can translate to billions of dollars in GDP and reductions in casualties. Carrier aviation is more than a small increase.
So to answer your first question (about the cats and drop tanks). DOT&E has no filter. Their world is black and white. It either passes or it doesn't against either the CDD or testing in an an operational environment. They will sit in the room with decision makers and state "not suitable". God bless the acquisition process because in the end, theirs is only an opinion that the Milestone Decision Authority (The one that says keep going, stop or need a new plan) will consider. I firmly believe that the program office responsible for EMALS, General Atomics, NAVAIR engineers (and probably NAVSEA) will solve this problem.
The answer to your second question is, "No, it's not $40B". It is going to be a different number for all of the aforementioned opinions offered and more. There are a lot of folks involved watching the cost, performance and schedule and I am confident that in the end the right decisions will be made and there will be happy people and unhappy people and reporters love to tell the stories of the unhappy because people like to read unhappy stories which increase readership which increases what the news media can charge for advertising which......sorry, I was digressing!
It will cost what it needs to cost so that we continue to maintain carrier aviation's critical contribution to total combat effectiveness.