Help! Rules 5.09(f), 7.08(f), and 7.09(m)

[Saltydog]

Dave H.,
I'm 'good-to-go' on the ruling... in fact, this has been a great primer on this topic which has been cut and pasted for future use However, I still don't understand the 'why'. ie. If F3 missed the ball and F4 had opportunity, but the ball hit R1... then an advantage was taken from the defense. So I can see the 'why' here. But what is the 'why' rational for the ruling when the defense isn't disavantaged? Ie. Your 'Bonds shift' example. Geez in that case the runner may have actually helped the defense by possibly keeping the ball in the infield.
Just tying to make (common) sense of the ruling. (If the 'best answer' is "just because", well, I can deal with that too!)
SD