I see your point, except that in this case, the organisation being gamed (the credit card provider) has no way of knowing if tax was overpaid or not. The point I was making earlier is that all the credit card provide knows is that you have paid $x to the ATO. So IMHO, if anything is going to cause a credit card provider to rethink awarding points on ATO transactions, it's simply the amount of points they are dishing out. In other words, someone paying the ATO $500k per year is more likely to cause a problem than someone paying $50k. Whether either or both of those people are overpaying, underpaying or paying precisely the right amount of tax is irrelevant from the credit card provider's perspective. Even if it's true that card providers lose money when awarding points on ATO transactions (something I have always found hard to believe), then they will be bothered by anyone paying the ATO large amounts, whether those amounts are due to the ATO or not. On the other hand, if the card provider breaks even or better on ATO transactions, they will either not care either way, or be quite happy for people to pay more than they have to.
Wrt the ATO - as I said I'm not convinced this would concern them greatly, but even if it did, how would they go about shutting this down? By refusing to accept credit card payments any more? That would not be in their interests, so I can't see that happening. It's possible they might start to scrutinise individuals who keep mysteriously overpaying tax, and as Burmans said they could probably make life difficult for those people, but that wouldn't have any impact on anyone else.