I have a roughneck DWC going right now.. Check my journal for more info..
The main reason you can't use the cloner all the way through is the weight of the plant. In the cloner, the plants are held in by little pieces of foam, once the plant weighs enough, that little bit of foam won't hold it in. Also the foam will strangle the stock.. Getting them in to netpots is the only way to keep them in DWC..
As for how close you can get them, as close as you want.. But they will shade each other, Fight for light, and the smaller ones won't get much light or yield much bud. If you don't mind training them (SCROG or LST) you can just choose a strain that doesn't get to bushy and manipulate them.. Otherwise you'll want room between them just for the sole purpose of giving them each good light. I personally like them close together cause I can get more in a small area.. I've got 5 nuken (a very bushy strain) in one tote. They are all up in each others shit all the time. I just keep trimming them so they don't shade each other too much..
Also you have to remember, the more holes and weight you put on that lid, the more it will bow.. If there are too many holes and too much weight, the lid will bow so much, the middle plants will be fully submerged and you're water level will have to be so low that the plants on the edges will be 3 - 4 inches away from the water.. That mean less water in your tote.. You might want to do 2 or 3 smaller totes..
As for the roots, don't worry about it. Like in any pot, the plants will only grow to the size of the pot.. Once the roots run out of room, the plant stops growing..
Good luck man! Happy growing.