In answer to this question.
1.No the stopper does not have to fit into the hole.
2.If you use this style of tank and you don't fit the stopper through the hole it would be a good idea to make a brace from scrap balsa to prevent the tank from sliding too far forward and pinch the fuel lines.
3.If you don't fit the stopper through the hole it is a good idea to seal off the big hole to keep fuel residue from getting inside your fuselage.