NAB
Unfortunately, no-one had updated the Long Term Costings against these larger ships
Nail on head. DGA(N) HQ (the Navy's aircraft people, but who had a Ships and Bases section) stopped doing this in 1988 as a result of the Hallifax savings. This created the Aircraft Support Executive (sans ship section) whose role became one of "monitoring" instead of "managing". Thereafter, MoD(PE) became responsible by default for accurately stating and costing all requirements; and taking the hit when they got the former, and therefore the latter, wrong.
To take the Mk7 as an example again, and very similar to the carrier, well in to the production phase the RN still expected it to be a mere minor transmitter power upgrade, as per the original endorsement. (The Tx design was finished in 1990, but then shelved as other programmes took priority). Their planning assumed whole fleet conversion over a single week-end at Culdrose. It actually took 3 years, during which time a dual fleet was operated. The problem (from a procurer's viewpoint) was, and remains, Requirements capture and articulation. You can't accurately cost and contract a programme if the Customer flatly refuses to support you. When that HQ shut down in early 1988, it took many years - perhaps 10 - for the RN to replace the Requirements Manager posts, and even then few were trained. Certainly none of the aircraft/equipment ones. And none did the old LTC job. And still don't.