No, the game and amiibo don't even take up half the space in the box.. They could've easily put the game directly behind the amiibo, and then made the box long and thin, but for some reason they made it into some massive cube?
And the yarn yoshi amiibo aren't even that much bigger than the figure amiibo. Their boxes are actually smaller than the smash ones, so it's nothing to do with the size of the amiibo itself.
I honestly didn't see the packaging myself, I just noticed the difference between the yarn yoshi amiibo size compared to all other amiibos