1. No, but it doesn't matter. You can use nothing under the grid, you can use water, perlite, a towel, newspaper, vermiculite, etc etc, its doesn't affect anything. The air is saturated (100% RH), none of that stuff matters.
2. Distance from the water doesn’t really matter, as long as the water isn’t touching the nest box, allowing the heat to travel conductively. You DON’T want conductive heat when incubating eggs. I don’t stack them because then it’s a pain to get at the ones at the bottom, and defeats the purpose of using the glass as a lid to view the eggs (without having to lat the cold air rush in). There’s no stratification of the air with regards to temperature. The incubator is only 2 feet tall, and 16 inches of that is water. He lid fits almost right with the top of the glass on top of the egg boxes.
3. 2 clutches will hatch at the same time if laid at the same time. Sure. But I purposely don’t put those clutches together. I don’t want a mix up to happen with say normal babies, and then het babies. Not worth it.
Cheers!! 
Jeff F.
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