The difference is that baseball lends itself to modelling. First, the game itself is very simple in structure with discrete elements that can be analysed independently. Second, the baseball season is 162 games long and each player appears multiple times at bat (or on the mound) in each game. That means sample sizes become large enough to be reliable very quickly.
Rugby is completely different. I'd think of it as a lot more like basketball, which is also difficult to model because so much changes with every 'event' on the court. Even American football is somewhat simpler, because of the discrete plays. Rugby is also affected by variables like pitch condition and referee style which further impact the reliability of sample sizes. RuckingGoodStats has written some good posts on this that I don't have time to dig up.
I have no doubt that teams are using a lot more statistics than we know about, but I highly doubt it approaches anything like the Moneyball model. More likely, teams track a lot of basic and advanced stats, some might even have advanced evaluation stats like baseball's VORP or basketball's PER, but this would be strongly balanced by subjective player-ratings, preferences for playing style, existing personnel (i.e. if you have Quade Cooper, you play an attacking, countering game), and so on. In other words, I would expect most teams emphasise traditional scouting and statistics, supplemented by statistical valuations as a way of reality-checking what they see, or to uncover hidden value. There are areas in which statistic would be extremely helpful, such as tracking success rates of kickers based on field positions. Captains probably learn those probabilities and use them to help make decisions about place-kicking.