The sim did what it should have done. It saw a SP right up against his target pitch count and with a middle-of-the-road pull rating, and it also saw a designated closer in the bullpen. In this circumstance, a higher target pitch count, a pull rating of 1, and no designated closer would have made it more probable the sim would have sent the SP out for the 9th.
The more important question, though, is what's best for the 162-game long haul: The settings as you have them or settings that would have made a complete game more likely in this one specific instance? Only you can decide that.