Looking at the exact situation you brought up earlier, Man on 2nd, one out. The average number of runs scored in this situation is .721, pretty good. Your chance of scoring one run is almost 42%. So you do what you're "supposed" to do and hit a ground ball to second, making the second out while moving the runner to third. With a runner on third and two out, the run scoring average goes down to .385. Had you struck out, your team is worse off, but not by much. With runner on 2nd two out, the run scoring average is .348.
There's never been any coach in the world asking their players to ground out to the right side(making the second out) to move the runner over to third. Ever. I said that if you were going to make the second out, you are better off moving the guy to third with a grounder than striking out, your odds are better at scoring. I see your percentages agree with me.