If you checkmark Remove for Defensive Sub with Lead, at least Hal always obeys. You are right in that it does leave the shifting to Hal, which can be a gamble. (Don't you love it when he throws a bench dude onto the field and then immediately replaces the dude with another dude, burning 2 bench guys?)
OTOH, there is absolutely no way of knowing how or when Hal will use
any of your Team Strategy settings. For example, is there any point at all to listing a Pinch Runner? And what is the point of the Infield In setting? Does ATG even convert gb+ to SI** with Infield In, like in the board game? I have used it to try to defend against a small-ball team, but I chuckle to myself when changing it from the default 3rd Inning all the way to 1st Inning. "Ah, THIS will stop Cobb all right!"