If teams do not hold on the runner because of their defensive shifts then this is just going to happen. We'll probably see some steals of home before the pitcher is halfway through their windup.
Solution of course is to play the 3B in the vicinity of the bag, though I imagine some sort of timing play with the 3B would be risky. At least the SS and 2B occasionally practice that. This is kind of like scratching your head as to why players did not try to hit to the opposite field when there were no fielders there. It is one example of the unanticipated consequences of analytics. If fielders are put into awkward positions to make plays they don't practice much, they are just going to mess up more of them.
