I work at a financial services company. There is NO WAY IN HELL that the IRS has a working reconciliation process. Hundreds of millions of paper forms with tens of billions of scribbled numbers. Paper checks in the mail system. Imagine trying to close the books at EOY.
As it was explained to me: “Yeah there’s no one in charge of checking if any returns are blocked because of duplicates, but that’s why we have people who listen to complaining accountants, right?” (10 months of limbo later...)