That's the result of adding fleet R&D cost to fleet build per-unit costs, to get the total program cost per unit, and then dividing the resulting total cost per unit among the parts.

If you spend $2 billion on R&D, and build 32 ships at $250 million each ($8 billion), you spend $10 billion for 32 ships = $320 million each, *program cost*.

If you spend your $2 billion on R&D, and then decide to cut costs and only build 3 ships (and get charged $335 million each because you lose your discount for quantity), you spend $3 billion for 3 ships = $1 billion each, program cost.

All that money gets spent on R&D, and design changes, and testing those design changes, and then integrating the new design parts into the existing ship design.

(Sort of like how the navy's railgun and electromagnetic aircraft catapult development get charged against the ship design rather than as an independent program.

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