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

Anche io di solito metto meno terra nel vaso, così da poterne aggiungere un po' per sistemare un'eventuale stretching del germoglio :) Ma non aggiungo mai terra se si tratta di una talea, in quel caso riempio al massimo il vaso direttamente, perché le talee hanno il difetto di soffrire (non sempre) di marciume al colletto :)

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?