The article even points out that an additional B2 Bomber would cost an additional 700 million not the reported cost of 2 billion. Including R&D costs makes sense in some situations, but not when buying one more.
"when the contractors allocated their engineering expenses among the individual spare parts on the list... they simply treated every item the same"
Sounds like an extra hammer would have cost an $15+$420=$435. Anyways, we'll never know.
I will say, the one thing I believe, is that the government had a bucket of money to spend on the project. Let's say it was $1 million. And the contractor was going to get all of it, all $1 million. Not a penny more and not a penny less.
And so you can't really trust the invoice is accurate except for the total being the budget available to spend.
If they needed 2 hammers then both hammers would have cost less. Thus rather than 2 * 435$ hammers + other junk you get 2 * 430$ hammers + other junk which is also 5$ cheaper (or whatever the actual number works out to.) Net result a total that’s 15$ higher and a different set of otherwise meaningless numbers.
R&D expenses are one time costs, they're not charged multiple times. An extra hammer would have cost $15.