Sorry mods this is a very big necro but I couldn't help myself, I've spent way too long trying to figure this out.
When I first saw this post I was also amazed and realized there must have been some trick.
Through the animation, the particles decrease, so there is some layering involved. The whole thing is also done in EHOLE, meaning there are more than 7 layers (to prevent black hole from forming).
Every yellow "block" has a black "block" layered directly on top of it, with the black one having 2 life less than the yellow one.
Every 2 frames, the current block dissappears at the same time the next black block does, so there is a jump from one position to another.
The framerate of the animation is about exactly half of the game's fps.
I figured this out in 2016, and made a few saves demonstating it, but it was pretty bad, and my process was really difficult. Coming back to this right now, I rediscovered the process and made a slight modification to simulation.cpp to make it much easier to do. If you comment out lines 141-155, pasting elements does not remove the layers below.
Here is a quick example I made with a frame jump of 5 instead of 2 because I was lazy.
Also, I should have used EHOLE. Some of my other saves have examples of what happens if you do this in the wrong order.
I still think it would be much too difficult to do what the original guy did without some kind of tool to draw and rotate rectangles and plan out the animation.