That's kinda the whole point of that storyline, if Tommy just wanted to fuck Josy it would make her the same as every other girl in the game, but that's clearly not the case. Tommy almost cracked when you talk to him at the bar, I believe it's the second stripclub visit, if you stay with Derek instead of Sage/Bella, but then just says "you wouldn't understand".
He is very obviously madly in love with Josy, and it's probably the first time he ever felt that way and the fact that she is his step-sister makes it all the more difficult for him.
I agree, that there will never be a path that explores a sexual relationship between them, but I have no doubt that Tommy will confess to the MC at one point and maybe the MC can at least make sure that those two reconcile and have a somewhat normal brother-sister relationship.