It may contain mineral salts, over time this affects ph. As well any nutrients left over may not be ideal for other uses. However, I do allow excess water left in the tray from the initial watering to be soaked up by roots. If a medium isn't fully saturated when watered, channels created in the medium hinder the absorption of water and it just runs right out. Many people mistake this for runoff so advise a heavier runoff percentage, but less water and slower is more efficient.
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