I decided to break the rules and turn on the autopots right after transplant when the seedlings were still tiny - 2" max. Worked great, no ill effects, don't listen to what they tell you. I don't think there's any need to wait until they're like 5" tall.
@BigDaddyK, It's all good - I'm hanging it up with this RDWC, though. I'm growing in a garage in the desert and to keep the water temp low I'll have blast the A/C. I'm buying more autopots and packing this system up until December!