I'm not all that familiar with Waitzkin's story. Pretty sure I met him back him in the day, but we certainly didn't talk about this stuff back then. And I haven't read that book. If you can give me some specific events, I could offer an opinion. That said, I'm not certain how much of a say he had (or profits he shared) in the book/movie based on him. Purely a gut reaction but I suspect there was at least some garden variety exploitation going on.
"At some point this may just be the nature of competing at the highest levels, but early scholastic chess shouldn't be that point."
Unfortunately, a little-discussed aspect of top level chess is that the only real way to be a contender for the world championships, especially these days, is to start young. Chess mastery is like fluency in a language - you can learn it at any age, but to attain the absolute top levels of performance you need to be a native speaker. This is probably why the cult of prodigies continues despite its downsides. In chess, music, dance, etc. people just love seeing superhuman performance.
"Perhaps part of it is cultural. I grew up playing in Russia"
I think you're right about this. Chess culture in the US is absolutely, positively terrible compared to other countries. I know that it's much better/healthier in Europe. I'm aware that it's a major cultural thing in Russia so I have to believe that it's better over there. Almost like a mental martial art, as opposed to whatever it is in the US.