(Rarity): "Does that mean I can see their organs and stuff?"
(Shining Armour): "They probably have the same index of refraction; so those can be partially invisible too."
"But what about the food they eat? That's not opaque."
"Hey, I just discovered this race a few days ago. I have no clue! It's like the toaster; bread comes in toast comes out. You can't explain that!"
"Oh. Are the crystal ponies' houses part invisible too?"
"If that's the case, I'd imagine they'd have to change in their basement."