If I was to consider the small seedling pot my "net pot", then keeping it ~ 1/2" above the water level is what I have been doing. At the beginning of this post the consensus was that I was essentially drowning the plant because I had the water level higher. The root ball has continued to grow and thicken over the past two weeks, but they just aren't wanting to dive into the water and continue to grow vigorously. I figured the agitation of the air stone bubble, being directly under the plant may have kept the roots at bay, so I move the air stone disk to the side of the pail yesterday.
As with pretty much anything about agriculture, there are no "magic numbers" for net pot height. General guidelines work pretty well, one reason being that there are so many variables that it's impossible for an individual grower to do everything "correctly". It's a plant and mostly grown from seeds and growers fuck things up so there's lot of opportunity for things to not to work out perfectly.
If your level is "pretty close" to the net pot, you're good. I set it at ½" and that's worked well for me. If you want to go with 2" or 6" that will probably work to well, too but there's no reason to drop water levels to 6" and, when you do, you're reducing the amount of root mass that can function as roots.
This diagram illustrates the parameters of the grow environment. I use this as a checklist and found it helpful in improving my processes.
For me, the big dog is light because light drives growth and then temperature and RH in second and third place. Yeh, genetics is important (if your seeds or clones are sickly then your SOL) but the rest of these factors are really way below those top three.
