Fellow beginner here I can speak from the research I’ve done that roots do not like light so the any roota sticking out of the pellet will just stop growing until you put it into a bigger container of soil. On my first attempt at growing I used pete pellets but soon found some fail to allow roots through, which ends up stunting the growth! Imo I would germinate in paper towel till taproot is about an inch or 3/4 of an inch then place it right into a cup of soil root pointing down. Everyone has there own way but I think you will have better success rate.
You need to put those seedlings into their own pots like right now.
Are you planning on putting all those plants in that one box?