I'm not sure you're going to get an answer at the level you want. You need someone to inspect the raw XML file that gets transmitted to the IRS, or read the instructions for tax software providers for the modified e-file system at the IRS web site.
https://www.irs.gov/e-file-providers/modernized-e-file-mef-user-guides-and-publications
While I don't know if the EIN is reported with the 1099, I suspect it is. So the computer is going to see a 1099 in their system that does not have a matching entry on your tax return. But the computer will also see an entry on a different line in the exact same dollar amount. I have no idea how good the computer is at spotting this kind of situation, this can't be the only time that something is reported on the wrong line of the return. It may be that if the gross income adds up right, it ignores line swaps. What you really want to know is how clever is the IRS computer, and you probably won't get an answer on that unless you teach yourself COBOL (a dead computer language from the 1960s) and get hired as a programmer.
As a practical matter, if taxpayer A did get a letter (automated) suggesting that they failed to report a 1099-MISC, they could reply by similar letter that the income was gambling, was reported as winnings, and an appropriate itemized deduction was taken. Taxpayer A might send a letter, fax or email to the casino asking them to cancel the 1099 and issue a W-2G. They would probably refuse (if they replied at all), but A could include that documentation with their letter as proof they tried to do the right thing. The IRS is ultimately going to see the gambling winnings and losses properly reported, even if the computer sends an automated letter at first.
