Why is the height determined from the floor to the bottom of the ball, rather than the middle or top

I assume you are referring to some problem involving a ball dropping to the floor? In general you need to be consistent in measurements, and measuring from the floor to the bottom of the ball is consistent in that when the ball hits the floor it's the bottom of the ball that touches the floor. Neither the middle nor the top of the ball ever touch the floor, so these aren't good choices to measure from the floor to.