moved into the soil

I'm not understanding the problem here... if it went through the paper towel and into the soil, I'd sprinkle a little bit more soil on top of everything - the paper, the seed (cover it all with maybe 1/4" of soil - and let it continue to germinate. The paper towel will eventually decompose and even if it doesn't, it's not going to be any problem whatsoever... Good luck!

You must very carefully open the shell, otherwise you will spoil the sprout

I usually put less soil in the pot too, so I can add a bit more to fix any stretching of the seedling :) But I never add soil if it's a cutting; in that case, I fill the pot to the max right away, because cuttings have the downside of sometimes suffering from collar rot :)

Why not fill your pots right up and provide maximum room for root growth?? A plant can only grow as big and fast as the roots can support. After all, the soil is generally the cheapest part of any grow, so why skimp on it?