You guys really have to read between the lines to come up with these explanations. What inclination has Montoyo given that he's using advanced stats to manage the team, maybe other than shifts which I'm sure an assistant is calling out anyway? Even Yost does that.
When asked about bunting he talks in "small ball" platitudes. Maybe Atkins is the smartest guy in the room and has cracked the code and found that bunting works and that's why Montoyo does it even with runners in scoring position. But I think the other more plausible explanation is that our manager is an idiot.