I think high velocity is partly genetic, partly the result of applying yourself.
Not every one can hit 90, but a lot more could than do.
I suspect someone at your high school, or perhaps a private coach they shared, knew how to get guys to maximize their potential.
What you may see at times is someone works at raising their ceiling in a workout bullpen. Later, they pitch in game circumstances and they don't focus on throwing hard, just on executing the pitch. As throwing hard becomes more and more the norm for them, and as their musculature grows stronger to get more done, the game MPH goes up as well. Obviously I cannot know for sure but what TPM reports as to her son's experience fits this pattern.
As for a guy like Jess Todd, it's also not uncommon for guys to lose some MPH as they move forward in pro ball. Sometimes this is an impact of pitching every fifth day instead of once a week. Sometimes you just wear down. Sometimes you stop throwing max effort all the time in order to focus on your other stuff or to try to improve movement and command.
Personally, having worked both with HS age kids and younger kids, I am constantly amazed at how many kids simply do not throw properly. A lot of guys start out doing something quirky and just resist every attempt to get them on track. Sometimes they end up pitching and they become that funky off speed guy, so they never even really try to maximize their velocity. If you give me 50 youth players drawn at random, and if every one of them would do exactly as I asked, I could raise their average MPH significantly in a 6-month period, no doubt in my mind. But in real life, 10 of them would refuse, 10 of them would have their parents send me nasty e-mails telling me off on one theory or the other, 10 of them would abandon the program, 10 of them would show some improvement and 10 of them would show a lot of improvement.
The most genetically gifted out of those last 10 make up the Jess Todds and Logan Chitwoods of the world.