I personally have not had a problem with it. I use those rapid rooter starter plugs so maybe they are protected from light etc....however I can easily see the sprouting seeds if I look so I'm sure they are not light protected. You are right to want to do things the correct way and I'm not helping you with that am I? But I have honestly never had a problem with it. You might start your darkness now and just tell the seeds that the pre germinating party is now over and they need to get to work.