Sphere is spawned on the cube face and pass through. Sphere.position.y value changed and that value is kept for all instances, giving on offset to all of them.
I think it’s more safe to create mesh with position at (0,0,0) and add an instance to keep root position unchanged.
I think I got it now: I understand the problem is that, if using thin instances, the root should stay at 0,0,0. But since I have to make root a physics body, it then changes the position of root - violating the 0,0,0-rule.
Why the 0-rule? Thin instances of root will get root’s position as offset right into their vertex data (once when creating). So as long as root is falling, I would have to correct the changes in position within the thin instance’s matrix. Since this is expensive, better keep root at position 0,0,0.
To achieve that on physics level I had to set mass to 0 when instantiating the physics body. Then when adding a thin instance set mass to 1 (or whatever) to that instance via the index parameter.
For some reason setMotionType did not work (STATIC to root, DYNAMIC to instances)