If I'm not mistaken, Advanced Map (If that's what it's called) can add those models into the existing overworlds,
and with script editors, can add encounters to those models.
I made a map previously, so that a Regirock doll (that looks more like a Regirock than the one in the cave) will give a Regirock encounter. (an entire room of legendary encounters)
That is a way you can add them in to Pokemon Emerald