I would think it wouldn't matter whether your ground sheet is under the netting or on top of it. It would be a lot harder to move the ground sheet around for varying conditions, such as windblown rain, if it's outside the tent.
For those of us with dogs, though, it would be almost essential to have the ground sheet on top to protect the netting from dog claws. I clip my dog's claws frequently, so I have not had any trouble with their snagging the netting or floor on Tarptents. In a Tarptent, though, he's not actually walking around on the netting as he would be in the Hexamid.