College pitchers from CWS teams have an almost unique injury risk, compared to the other categories studied. This would naturally have gotten worse, because the draft was moved earlier in the summer.
It also makes sense that a "Moneyball advantage" can only exist as a significant advantage prior to being pointed out and carefully studied by researchers as well as probably all scouting departments. With the expansion of baseball analytics, fewer factors will be left unexplored and not thoroughly correlated. I'm sure there was a time when pull hitters (like Ryan Howard) who didn't effectively make use of the whole field on both ground and fly balls were over-valued after "the shift" became a big thing. I'd be surprised if that wasn't fully taken into account today.
Where this article falls down, IMHO, is by classifying players by draft position rather than by size of bonus. In the end, it is bonus $ which are the limiting factor in this era of the hard cap. H.S. draftees have the most bargaining power; college seniors and red-shirt juniors have the least bargaining power. Judged on a WAR/$ basis, college seniors or red-shirt juniors might be the best bargains, although modern analytics likely closed that gap within a year of hard caps being implemented. It's these rule changes which open up the opportunity for at least a small measure of at least temporary advantage. The extra year of protection prior to Rule 5 draft exposure would seem to benefit the value equation for H.S. and LA talent.
A potential source of great advantage is having team executives who can predict the next rule change, prior to most teams knowing it will happen, and changing their talent acquisition model accordingly. The rules for acquiring international talent have just undergone a major change. The Phillies appear to have been caught flat-footed by that one. It would be a big plus to have a one draft/off-season head-start in knowing when the NL is going to adopt the DH. Makes some sluggers a lot more valuable to an NL team. Changes in the strike zone favor or harm different types of hitters. A switch to mechanical determination of balls and strikes will change the evaluation of catchers' defensive abilities. All of these changes and others, like expanding roster size, the hop-hop change to the balk rule, enforcing the maximum time between pitches, eliminating the phantom out at 2B on a DP, and the recent change to draft comp for FA traded during their FA year can greatly change the relative value of individual players and prospects. Of course PEDs are the elephant in the room. The system can still be beaten and is still designed to be beatable. That could change.