You can't call it the percentage play after the fact. You could just as easily say we didn't score so it was the wrong decision. With our hitters, I would rather have 3 chances to get a hit to drive in the run than 2 chances to get a hit, passed ball, etc. to score a run. But in that particular situation, the odds are so close you can't say either bunt or hit away is the "right" or "wrong" call. And that situation is the best of the potential bunt situations. In almost all other situations, it is the wrong call.
You are ignoring the fact that bunts for base hits happen, errors happen on the throw to first, etc. All of that more or less offsets the odds that you don’t get the bunt down. We made a call to increase our odds of scoring by (at very least) 3% by executing a fundamental play, and we did so successfully.
That 3% is also a composite figure assuming the average of any hitter at the plate (whether it be the 9-hole, 2-hole, or leadoff guy). If you look at runner on 3rd with less than 2 outs for the top of the order vs runner on 2nd with no outs for the 9-hole, I’d bet the odds are a lot more in favor of the winning run scoring in the first situation. This is just another case of sabermetrics painting with too broad of a brush in some cases. You have to know when to use the data and you have to know when to use common sense. Every pro, college, and high school coach in the country is bunting the winning run from 2nd to 3rd with no outs and the 9-hole guy up there. Every one of them.
ETA: They also put a graphic up that showed Gilbert’s average with RISP was .236. He has a 25 K’s in 100 AB (.250 percentage). So you can clearly see that the odds of him striking out or otherwise putting the ball in play without a hit and without moving the runner is way higher than him getting a hit in that situation. Yet another data point that indicates the bunt is the correct play.