Ray Allen, Reggie Miller, Michael Redd, Larry Bird, Mitch Richmond, Steve Kerr....and so on....
For every example you give, one can be given to counteract. And the research Tangosz did backs this up as no correlation was found between FG% and FT%. Being an excellent shooter doesn't guarantee free throw proficiency and the opposite is also true. While the form is the same in any type of shot, free throws are markedly different from a jump shot.
Of course, anyone with a modicum of shooting ability will be able to attain a certain level of free throw proficiency. This doesn't change the fact that the two shots are markedly different, requiring repetitive practice and contrasting form.
If the purpose of this game is to mirror real life, then it is certainly ridiculous to have atrocious free throw shooting while simultaneously having above average jump shooting. But to suggest, as it seems you are, that jump shooting and free throws should be perfectly synced is equally ridiculous.