I have personally tried every way you just mentioned and I have never had great success with rockwool cubes sitting directly in the tray (even in a botonicare tray with troughs). I did however have good results going from 1" rockwool cubes into 2.75 litter individual pots filled with hydroton.
The hydroton allows the roots to get more oxygen and is much harder to overwater then rockwool cubes sitting in a flood table. Rockwool tends to retain a lot of water, so when the table is flooded for 15 minutes the entire cube is saturated which takes a long time to dry. This is not too much of a problem provided you allow plenty of time for the cube to dry out. An excessively saturated rockwool cube doesn't deprive the roots enough (if that makes sense). Roots that are deprived excessive amounts of water search for water, and therefore grow more vastly.
Otoh, explanded clay doesnt retain as much water, so it can be watered more frequently and dry out faster, which will provide more oxygen to the roots and promote vigorus root development.
My suggestion to you is this. It sound like you took cuttings and put them into small rockwool cubes to root. If this is so, allow the roots to develop on the clones. Once there are a good amount of roots coming out of the rockwool cubes transplant them into the 2.75 litter pots filled with hydroton, but when you do so place the clone high in the pot so that when you flood your table the water line just barely hits the bottom of the cubes. This will pull the roots down into the hydroton and you're all set! Roots that grow outside of the holes in the pots will air prune and that is fine! It sounds like you use very little if any veg time if you are harvesting every month so your plants will mature just fine in the 2.75 litter pots. You will be surprised how much air pruned roots can explode inside of these pots! I bet when you pull them out at the end that the hydroton is completely supported by the roots and it all comes out in one piece!
Sorry I started to babble there... anyway, I would go with this method. It has produced much better results for me than rockwool sitting in a tray. I also perfer individual pots over large beds of medium (like: filling your tray with hydroton, or coco mats, or STG mats). With large beds like this you cannot move your girls around, and plants tend to find sitting water in your tray and that has caused root rot for me
Well I'm gonna stop babbling. I think you got my opinion.
I will say though, that I've seen successful grows using the methods I discouraged (or ripped on... sorry), and I am nowhere near an expert! But I can share my experiences.
GOOD LUCK TO YOU!
PS If you go with individual pots with hydroton, you MIGHT need to find something to lift the pots up just a tiny bit so that water is able to fill the pot from the hoes in the bottom and roots are able to escape and be air pruned.