About 10 years ago - in February 2016 - I posted a story about the 2004 Thomas Edison Collector's Set and mentioned the potential of additional profit to be derived by the United States ("US") Mint from the Set's higher selling price vs. the standalone coin that it included. This spurred a question about the extra funds regarding "where" they went. I try to answer questions that my posts generate, but clearly don't always do so in a timely manner!

I did answer the question via other posts, but did not tie my replies directly to the 2004 Thomas Edison Collector's Set. So, the answer might have been overlooked. (To review the original, question-generating post, see:
2004 Thomas Alva Edison Collector's Set.)
The short answer to the "money" question is 'Public Enterprise Fund.'
Quoting from an earlier post of mine:
" in October of 1992, as part of the law that authorized the 1996 Atlanta Centennial commemorative coin program, the US Mint Public Enterprise Fund ("PEF") was established. The PEF provides greater financial flexibility to the Treasury Department and, by extension, the US Mint, in terms of the availability of funds it needs for its operations. The Fund removes the need for annual appropriations to the Mint and removes fiscal year limitations on money needed by the Treasury/US Mint for its operations. Basically, it enables the Mint to self-fund its operations and use the money it generates as the need for it arises. The Mint does so by depositing all receipts (money) it receives through the sale of circulation coins to Federal Reserve Banks, commemorative coins, bullion coins, medals, numismatic accessories, etc. into the Fund and then drawing from the Fund to pay its expenses. Funds that are determined to be in excess of what is needed to run the Mint's operations/business are transferred to the General Fund of the US Treasury.
"The language of the PEF law (which took effect beginning with the Mint's 1996 fiscal year), requires that all receipts from "the production and sale of numismatic items be deposited into the PEF. It defines numismatic item as 'any medal, proof coin, uncirculated coin, bullion coin, numismatic collectible, other monetary issuances and products and accessories related to any such medal or coin.'"With the PEF in place at the time of the 2004 Thomas Edison commemorative coin program, revenue the Mint derived from sales of the Edison Collector's Set (and any potential profits) were deposited into the PEF and available for the Mint's use as needed. Once deposited in the PEF, revenue is not generally tied to the specific coin program that generated it, but rather just part of the general fund.
2004 Thomas Alva Edison Silver Dollar

For a PEF-related topic, see:
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"Numismatic Item" DefinitionFor other of my posts about commemorative coins and medals, including more modern commemorative coin stories, see:
Commems Collection