The hammer did indeed cost $435. If the government wanted to buy another one, the contractor would have charged them an extra $435. Just because the extra $420 was "R&D expense" for something else, doesn't make the hammer any cheaper.
Even in the most charitable explanation, this makes it impossible to know the real cost of anything. If the contractor can lump all sorts of charges into the cost of the hammer (for unrelated projects), it's a way of hiding the true cost of anything.
I've worked for companies where they took money meant for one thing, and used it for something else. "Can you record your hours on this project under this different expense code?" This stops them from going over budget and having to explain to the client, but takes the money from another project of that client instead.
The $435 hammer sounds like that. They didn't have R&D budget, but they had a hammer budget. Let's spend the $100,000 hammer budget.
About 20 years ago, a friend of mine worked on a contract for the Department of Defense in IT. He told me that he was making $1500 per day, and for the first few weeks, the government didn't have a computer for him. So he sat at a desk, reading "printed manuals" waiting for a computer to arrive. For weeks. Making $1500 per day.
The truth is worse than a $600 hammer.