I use both methods you mentioned. Pots of clay balls to test new strains and net pots suspended above tray for production SoG runs.
For clay balls you need to bury your stem lower in the pot and you only need to flood a couple inches up the pot. The roots will do the rest. You dont need the rockwool.
Otherwise you can just drop rooted clones in a net pot into holes cut in a lid for the tray and flood as much as you like. I do 30 mins on 30 mins off during lights on. It is closer to NFT than F&D when you do it this way:
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