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I wonder if the kind of drainage holes in the pot matter
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For an experiment? No, I wouldn't think so. As long as you get two of the same kind.
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Putting a permeable material under the soil makes sense for drainage to me...
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Exactly. That's the point. A
permeable, as opposed to an impermeable rock would be fine. Something like crushed rock wouldn't be good. It wouldn't allow liquid
through it so the water would have to squeeze through crevices and cracks, which would back up the water leaving a perched water table.
I agree with Dave about the different heights as well. I have holes drilled into the sides of my 5 gallon buckets, and my 4 gallon milk crates (which holds 5 gallons of soil, go figure) have triangular holes all up the sides and bottom, so I just punch holes in my trash bag liner all over. Easy to check soil moisture at different levels.
Since I'm VanGogh, I decided to draw a picture of a perched water table. The white lines are supposed to be roots with their feet wet. Feel free to snicker and guffaw at your leisure.
Plains