I'd always figured that Eta's flat costs were the total value of everything expended to make the item.
So they aren't paying 200 million per item to outside vendors, but rather she's expending 200 million worth of resources. Whether that's based on raw materials + labor hours or just what Gamma would've gotten if she'd been able to sell the components through Mitsugoshi, we have no idea.
And this is a comedy, so I doubt it'll ever actually be explained. (Unless we get a scene where a new Number just asks about it.)
Then saying it "costs millions-billions of zeni" is the wrong fit for situation.
In ordinary English, “X costs Y dollars” means someone paid (or would have to pay) that amount in a market transaction. In a commune with no wages, rent, R&D charges, or planned sale, that market sense does not apply.
If you want to describe opportunity cost of the materials: those components could have been exchanged for a billion dollars instead of being locked into a device for Shadow Garden's use that will be destroyed after one use. That is a real economic cost, but it is not the same as a purchase price.
So last chapter's "can we mass produce this?" "No. Each unit costs 2 billion zeni, and it breaks in one use" ought to be
"No. each unit uses materials worth 2 billion zeni and it breaks after one use.”
But none of the above matters because in this chapter Eta says "It only cost 200 million I"ll send you the bill later." What bill? It can't be your wage because they don't pay wage, it can't be 200 million worth of failed r&d experiments that lead to this working version, they'd all have been paid for during development. It can only be the components of this particular device actually costed her 200 million and she's having Alpha/Gamma pay for it.