Absolutely. The argument wasn't that they're exactly alike, it's that they're related. And I would argue that they're the 2 most related skills of all the trainable skills.
Because of that, my other point is that it makes a lot more sense to get a secondary pop from jump shot training with free throws than it does some of the skills that do.
I would actually argue that Jump Range and Jump Shot are the two most related. Whats the difference between a 17 ft shot, and a 24ft shot? Action wise, not much at all.
Free throws, in general, tend to be a non-jumping, fixed position shot, which is a different action to the normal jump shot. I know Crazy-eye said that you CAN jump when shooting free throws, but when was the last time you saw that? Last time i saw that in a game, I was 9, player junior basketball.
But overall im all for the current system. It works, gives Free Throws a certain 'place' of importance in the game.