If you imagine the universe is made of random real fundamental constants rather than random integer fundamental constants, then indeed there's no reason to expect such collisions. But if our universe starts from discrete foundations, then there may be no more satisfying explanation to this than there is to the question of, say, why the survival threshold and the reproduction threshold in Conway's Game of Life both involve the number 3. That's just how that universe is defined.
Why do you assume the two have to be small integers? There is nothing currently in physics which would disallow the electron to be -1 and the proton to be +1234567891011213141516171819. The fact they are both of magnitude 1 is a huge coincidence.