Furthermore, how do machines "fall short" compared to free weights from an athletic stand point?
The answer is not just free weights but how an exercise is performed.
Balancing the weight while standing involves many more muscles. Lifting weights while standing on your feet, pushing against an unsupported weight involves the muscles that align and support the spine.
Machines do not require you to balance the weight because you are pushing against a braced object.
For example, a barbell squat develops superior strength as compared to a leg press.
A standing barbell press develops superior strength compared to a machine press.
Spend your time doing machine presses and then try the same weight with a barbell. You'll fail.
So, it's really the way an exercise is performed. You could do free weight exercises in a supported fashion and get a less optimum result.
Some NFL teams jumped all over the Nautilus machines when they came out but after a few years of their players getting crushed by teams that used the old standbys (power cleans, barbell squats, free weight bench presses, etc.) those Nautilus machines were relegated to rehab/prehab.