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It can be done if the plants are spaced far enough apart. Only thing Id worry about is roots getting sucked up into the pump and having root bits clogging the sprayers up, not to mention the thrashing the roots would take.
You could do it, but I definitely wouldn't recommend it. There are a lot of hydro systems actually designed to flower with that would be much more suitable. The EZ Clone is the shit for rooting cuttings though!!
Cork, what makes you think they'd mold? Keep the humidity in check and it's no different than any other aero system, at least above the lid.
It would be really nice for uni harvests, prolly couldn't clone in the high PPMs needed for veg/flower.
I had the same idea for my DIY aero cloner but worried that the plants would get too heavy for neoprene collars. I think it could work if you bought a 2nd lid and drill some 2" holes in it with a hole saw and add net pots filled with hydroton. Maybe keep a bubbler in the standing water in case stray roots decide to venture too far south. I would make sure to keep to an appropriate aero watering schedule, too.
I haven't seen it done, I think you should try it with some spare clones and document it on here!