The tomato is a very delicate fruit that fears the cold. If you put it at the refrigerator, it will very quickly lose the little taste that it has (if it's a commercial tomato, which cannot compete with a home-grown tomato). So it's best simply to store them at room temperature.
According to the variety of tomatoes, and the thickness of skin, (home-grown tomatoes have thicker skins), it might be necessary to leave them in boiling water for a few seconds longer. In any case, never exceed 30 seconds, otherwise the tomatoes start to cook.
Some recipes suggest removing the core of the tomato before putting it into boiling water. I think this is a bad idea, because the water gets inside the tomato and reduces the flavour even more.