The problem isn't in timing functions. It appears whenever the "distance" involved in a transition is dynamic (rather than specified by the designer/developer).
a bit related, i remember a couple years ago complaining that jquery's "slow" and "fast" as shorthands for preset durations was misleading because when animating on a wide screen, "slow" ends up being quite fast compared to a narrow screen width. you are never really defining the animation rate, as was implied. this is of course due to the fact that everything is based on a fixed duration being passed into the supplied easing function.
Exactly. In a certain way, you could call jQuery UI effects a very limited physics engine.
I don't think the author is saying everyone should use a physics engine now. I think he means that we should use real-world physics as a guide to making more realistic animations, be it with a simple effects library or a full-fledged physics engine.