And there are real mice in the same "universe" that contains Mickey Mouse.
Some characters were human analogs and some weren't. Even if they were the same basic species.
But since the original appearance by Goofy was just as a throwaway character in a crowd scene (it was the laugh that caught Disney's tradition) things probably weren't well examined and then future designs were just based on the previous ones.
Here's Goofy in his first appearance:
Notice the human pig, goat, cow, and dog, with the more natural looking cat and dog. Ultimately I'd say that the "dogness" of Goofy is immune to logical consideration.