The above ground roots you're asking about are just the oldest, woodiest, more 'hardened-off' on the tree, and once they've gone completely woody, you can just remove soil down to where newer ones are (but don't leave them exposed). I'm not sure what you think planting seeds in rockwool (strange to begin with) has to do with planting on a rock, but generally root over rock trees are ones that have been grown for a while in soil and have established roots. They are then put onto rocks with muck, a combo of peat and clay (with a little water), then the whole thing (roots and rock) are wrapped with something like raffia, or loose elastic bands (just tight enough to hold the roots against the rock, but no more) and then put into a pot with soil to the rop. Over time (months) more and more soil is removed from the top down to expose roots as they harden up, until they've grown into the soil below the rock and the whole thing can be removed from the pot except for a base (shallow bonsai pot or slab). You keep the seeds in the fridge (in a baggie with only slightly dampened vermiculite or moss) for 90 days, then plant them in a 50/50 mix of peat and perlite well stirred with bits of water til it's just moist throughout, and finally transferred into regular bonsai soil in a pot. You're starting at the wrong end of the season, however, as anything that grows after the 90 days are up may well not be ready to go outside for next winter in time. And hinoki grow sooo slowly. Why not just pick up a small one at a garden centre and learn to keep it alive for a year?