I've had a little bit of experience with it during my stay in Poland, and my impression was that while the diminutive names were used frequently, they were by no means used exclusively. It would be mostly close friends and family using the diminutive name, and even they didn't do it consistently. One of the girls in my host family was called Zsuszana, and she was referred to by her family as Zsusza much of the time, but not always.

With Spanish names, as far as I'm aware, it depends. Some Francisco's are indeed known universally as Paco, others are only called that sometimes by some people.

My point is, it's one thing to have an official name and a nickname or diminutive, and to use both depending on the occasion. It's quite another to call someone one thing officially and never use that name in reality (or it'd have to be that horribly cliché American thing of parents using their children's full name, middle and last names included, when they're angry).

And so as you've presumably already deduced, I really can't see the harm in registering a child's name as "Tom" when you fully intend to call him Tom.