Bryant was pretty much built to hit flyballs. That was his MO from the get-go. The reality is that even in this day-and-age not every hitter is geared this way, and the organizations tend to let a player's natural abilities speak before they go trying to fix something that isn't broken, and they try to ease those types of suggestions in gradually rather than pervert the maturation process. I would rather have a high contact guy with strong EVs and talent for the sweet spot and tinker with his attack angle over time, than I would to take a flyball hitter who probably has some swing-and-miss and try to remedy that. But IDK, good players emerge from both scenarios, really. I don't think you should get so hung up on GBs for minor leaguers but I understand your concern. For a dude that was just drafted a couple months ago, though, it's nuts. This is the way he has hit his whole life and it's continuously working. He's doing something right at the plate. It's not like he's gonna be a bust if he's a high GB% guy, either.
Just this year Acuna is 15th in GB and Yandy Diaz, Yoshida, Wm Contreras, Yelich, Soto, and Nootbar are all in the top 15, and all are having excellent offensive seasons respectively. There's more than one way to skin a baseball.