Correct me if I’m wrong, but didn’t Minfilia’s body turn to aether/vanish when she pledged all of her being to big momma crystal? Perhaps returning in a smaller body is easier, uses less aether.

As for how she is back, she might have used the light from the flood of light to sneak her way back to The Source. Heck, the light from the flood could very well come from the same place, making for some interesting interaction between reflection and source.