Surely Bowser must have inherited his throne from someone, and given the durability of his species, I find it hard to believe his father managed to get killed while he was still a baby. What if he was around, and we just didn't see him? Heck, what if the castle from Partners in Time belonged to the prince, while the king had his own bigger castle somewhere else, and it was inherited to Bowser Jr in the present, hence why the face on it still looks young. Would make sense that the Koopa King would want his son to be raised in his own castle, grooming him in preparation for his time as king, and that would be Kamek's job to raise him.