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Small chick seems to jump just a bit higher. For example it can jump on the boxes on the first level while the big chick can't.

Thanks for comments! Actually it's just an illusion because they are all the same. Jumping on the boxed on the first level is a case with a small probability (which is intended).

Maybe they have different colliders? I wasn't able to jump on the boxes with the big chick even once

No, they have completely same colliders. It's true that it's harder to control the big one, but it's just because of illusion.