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Leaving a seedling alone is almost always the right answer. When you move the Rapid Rooter to soil, you can bury it deeper, and it will begin growing roots higher up the stem (I've read. I've only done that a couple times and never did post mortem to see what happened.).
FWIW: I used Rapid Rooters for awhile. I like them. I buried them in soil (20oz seedling cup) so the plant could grow directly into soil. (No trays and domes.). But, my impression was that RRs are made for cloning. The pre-made hole seemed way too large/deep for a seed. I would jab/poke/carve/enlarge a hole in the bottom. I'd bury the RR upside down, and insert the seed into this new, snug hole. I would pluck off some small pieces of RR material and lay it on top of the seed if it was too open/exposed.
I never did try germinating with the seed in the pre-made hole. I can't compare. But, I never had a problem with my way.
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