Let's say Flores had gotten a hit. Then when Cabrera had approached the plate Cincy would have protested. Cabrera would have been called out for batting after Nimmo. Cabrera's actual PA, taken by Flores, would have been erased. Bruce would have come up with two outs. Interestingly, in that situation Bruce is OK to bat because he is considered to be batting after "the legitimate batter" Flores who is considered never to have batted because Cabrera stole his spot. This despite the fact that Flores actually did something and Cabrera did nothing.
I like the rule and I'm pretty sure it makes sense, it's just really difficult at first.