That simulator just tells you if a trade is fair using projected WAR and projected/guaranteed salaries for the players involved. It can't accomodate whether players are clubhouse leaders/cancers or a GMs desire to keep or deal a player. And hey, sometimes GMs make bad trades. (Actually lots of times.)
Really what it does it gives you an idea if a trade is fair for both sides using the criteria previously discussed. I know a lot of people are poo-pooing it, but the old way for fans to propose trades was almost always lopsided. Go to the Yankee thread where Meh proposed the Yankees could get Syndergaard and Edwin Diaz for Miguel Andujar, Clint Frazier, Holder and Mike Ford. That's the classic "we can get anything for one really good player and table scraps that fill holes" proposals that still fill the internet to this day (and I've made them myself).
At the very least, BTV is objective and I keep kicking myself for not thinking of it first, especially since I have used a similar one on fantasyp.com for fantasy football trades...