Someone other than Steven or the player character wins in the "good" ending.When the player character touches Steven, it destroys them both but the phlebotinum reaction gives birth to a new character who promptly uses the box to go back in time and set the game in motion again.
The ending is all about looking back into childhood, and rediscovering dreams.Think about it. In the good ending's credit roll, it is said that someone (hopefully the player character) had a box in which he painted whatever he dreamt of. At the age of 10, light (a grasp of reality) came, and he realized that if he settled for one of those dreams, he would have to give up the others, therefore "killing" them. Trauma kicked in, and he tried to never ever think about it again. Then, fully-grown, the player character finds himself in a pointless life because in childhood he couldn't deal with the fact that you couldn't have all your dreams accomplished, and gave up dreams altogether. Then he finds his childhood box, full of dreams and alternate realities. As he looks through them, his memories of his inner child, repressed because of the trauma, come back. He develops Steven. At the end, he is able of not taking the pill (trying to escape again), and face Steven. His years have made him more mature, and he accepts that he cannot achieve every dream he ever thought of, but instead he can focus on one of them and accomplish it. By going out of the box, he remembers how unfortunate was his life, and how much the box helped him, wishing he could go back in time and tell himself to get over that way earlier. At the end, as he runs he duplicates himself. Every one of his copies belongs to a different dimension of reality, but in everyone of those he has settled for one dream, and nothing won't stop him on his way.