The only time that the bottom of the swing is guaranteed to be even with the left shoulder is when the left shoulder is stationary. However, this is not the case during the swing. There is no disagreement that the left shoulder is moving upwards during the swing, thus changing the bottom point of club path. It’s clear from the TM system figures that the clubhead is going UP at a 2.8 degree angle with respect to the ground. However, because his clubshaft is still bent forward, the club is moving DOWN with respect to the shoulder.
I’ve created a couple graphs to illustrate what I’m saying. In the first picture, the left shoulder is stationary (the red dot). Using excel, I have calculated the clubhead path assuming that the club and arm act as a straight line of fixed length. This path is shown in green. As expected, the bottom of the path is even with the left shoulder.
The second figure shows the path of the clubhead with an upward shoulder motion (the shoulder moves from the blue dot to the red dot.) The resulting path was calculated assuming that the shoulder moves upward at a constant rate, and that the club and arm act as a straight line of fixed length. As you can see, the path, shown in green, hits its lowest point well before it is even with the left shoulder. At any point between this bottom point and the point even with the left shoulder, the clubhead is traveling UPWARDS, but the clubshaft would still be leaning forward. This appears to be the case in the TM analysis shown above.
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This does not guarantee that the clubhead will be traveling upward for a driver, but does show how it is possible for the shaft to be leaning forward and the clubhead still travelling upward. If the left shoulder does not move upward very much (as Mickelson says he does), it would be quite possible to be hitting down on the driver.