Hi, I have an animal shed that has a roof that extends at least 2 blocks out over any of the grass blocks for my sheep, but every time a tornado comes around all the grass is turned to dirt.
So yea grass that has blocks over it will still be turned to dirt

I'm not sure if this is how it's intended in the mod, but IRL, that would happen. If your "shed" was completely walled in, then it would be different, but if it's just a roof, then yea, a tornado would totally damage the ground under that roof from the high winds that would be moving along the ground.