hmm, honestly now that i think about it, its probably not much different from any normal method of avoiding root rot. plus like zem said, not frying em with light. 'overwatering' (rot) and light are probably your only concerns. and not killing them with nutrients.
I forget who on here said it, but mentioned that you can just put germinated seeds with like, more than an inch tap root directly into a bubble/aero cloner directly in the neoprene collar. tried it with some bag seed and it worked totally fine. also have seen mentioned of people just putting seeds in rockwool directly into the system and just flooding/wetting it periodically (top-drip DWC, f+d, aero, bubble etc).
I've just started putting rockwool into those small 1.5" net cups into my garbage bubble cloner for various things. keeps em moist, but not soaking wet, and super oxygenated.
But ultimately, thats the worst case scenario right? Damps off (pyth), root rot (probably pyth), it dried out, or you killed it with lights or nutes.