I think free throws in the paint do count.
Given the usage in the related NBA sim of things like assist percentage and the like, I see no reason why they wouldn't use other versions of points in the paint where things like that DO count. Because, frankly, not including free throws from fouls in the paint is utterly stupid, even if the real life one does it that way. Those are points. They are earned in the paint, by drawing fouls, usually by putting yourself in good position.
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I also think that presuming the worst interpretation (That they are meaningless) Instead of the simpler and more likely explanation(They included free throws in the paint) is a bit unfair.