Yeah, it's probably as rare as it seems. Pretty simple, really. If a kid doesn't make it on one of the HS rosters as a freshman, he already wasn't good enough to make the cut to begin with and then he starts falling further behind every day the HS team practices, which is pretty much five days a week for 5-7 months. That's a lot of reps and progression that has to be overcome, even with extra instruction, training, etc.
I would guess that most of the exceptions are usually kids that go to big, deep powerhouse HS's and decide to transfer to smaller/less deep schools or, as you describe, kids that grow a lot and become pitching projects.
During HS years, I think baseball more than most sports requires daily reps and regular play (or at least situational simulation) to really advance, barring the few exceptionally gifted.