There are a lot of reasons why the animated examples couldn’t be built. For one, any system with multiple balls would get out of sync very quickly. But even with a single ball, the bouncing is such that a ball would almost immediately bounce in the wrong place and fly off. The very worst segments are when the balls are falling down a “shaft” with tubes on either side–even a tiny error would magnify after just a bounce or two.
You could have a design that constrains the motion somehow and plays a tune. A ball traveling down a slide and hitting things as it passes would be one example. But it wouldn’t look anything like these.
I’m not sure how “faked” these animated examples are. By that I mean they could have been designed to use the physics engine as-is, with the positions fine-tuned to give the expected results. Since computers are (mostly) deterministic, the artist could just tweak each note to be in just the right place. Tedious but doable. On the other hand, they could have just completely faked it, with the motion of the ball being totally constrained and it only vaguely acting in a physical manner.