The Tom Bombadil stories were separate from Middle Earth when Tolkien wrote them. Tom is just a cameo from Tolkiens other works. He’s a minor character put there because Tolkien liked him and thought he fit. For the sake of the story any elf could have done, Tolkien could have wrote in any major character or made up a new minor one. He chose Bombadil because he didn’t have a use anymore in his own, older stories and Tolkien wanted him to live on happily ever after in Middle Earth. Tom was first, those stories came first, he is Eldest, conceived before the first acorn of Middle Earth, before the trees and lamps. He lived on past the death of his own universe and settled in Middle Earth. That’s why is not affected by the laws of Middle Earth, his ways are older and stranger. Goldberry is a Maiar who knows all this.