There are lots and lots of legitimate refunds of this quantity. IRS doesn't have enough resources to look too hard at each one of them, as the wait time for refunds would then be unacceptable.
If you can’t prove the assertion don’t make the payment, no matter how many months that means people might have to wait.
Similarly, a simple cross-check to see if the refund is feasible considering the other filings by the same individual/entity.
Certain refunds cannot be cross-checked as easily by a computer (eg reclaiming VAT on purchased goods). But basic refund fraud on lotteries? That shouldn't really be a thing in almost 2020.
I presume that it's how they ultimately caught them.
Overall, I think that while your suggestions obviously make sense, it's probably pretty hard to theorize like this without knowing the reality on the ground. Maybe implementing systems like this is very slow and very expensive (like everything US government does), so we'll need to wait a few more years. Maybe it would result in too many false positives, which would seriously degrade its value. Maybe people who could implement this simply don't care, because it's not their money being stolen.