No, I don't get it. Because in the BB game, JS and JR control a players ability to hit jumpshots and 3 pointers. You are arguing that the real life FG% and 3P% don't influence FT%, why on earth should JS/JR be linked with FT in the game? That makes absolutely no sense at all.
If a player is so horrible at shooting FTs, but is good at jump shots, it doesn't take much brains for the player to shoot a jumpshot as his free throw. (A free throw shooter is allowed to jump, as long as he doesnt step over the FT line before the ball reaches the rim.)
Looking at the guy posted in the first page of this thread:
http://www.buzzerbeater.com/player/7095293/overview.aspxyou can see that he shoots 0% in over1000 free throws in his career, while this season he is shooting 0.483 from the field (I assume a lot of these are JS given the fact that he only plays PG) and 0.287 from 3-pt range (obviously jump shots--excluding any full-court buzzerbeating heaves) in over 350 attempts. This player has been around for 10 seasons already.
The reason players shoot FTs without jumping (jumping without a violation) is that it is easier to shoot a FT without jumping, because the motion of a FT is a more compact and more reproducible than the motion of a jumpshot. However, if for whatever reason, shooting a traditional FT is harder than a JS, then the player can (as long as he doesn't cause a violation) shoot a jumpshot for his FT. Thus, (even with nerves being factored in) it doesn't make any sense for a player's FT% to be drastically less than his JS%.
(Note that this is not an argument meant for logic. Making 0 FT in over a 1000 attempts is obviously illogical, unless the player is purposefully trying to miss by throwing the ball in the other direction.
This is an argument relating FT% to FG%--particularly for guards, who can have their FG% (or 3-PT) related to their JS%.)