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I'm having a hard time understanding how the drainage material causes the problem
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To be honest with you, so did I.
I have no idea if perlite would do the same, never tried it. Just rocks and sand.
Think of it like a 4 lane highway turning into a 2 lane. As the water searches for ways to go through the rocks, the remaining water backs up as it waits for it's chance to drain down. This causes standing water, which saturates the soil, which can encourage root rot and insects.
Again, I'm just relaying what the extension office is saying (like I could make up "perched water table").
Good growing all,
Plains