So where is the problem? Nolan himself has said in media interviews that the significance of the top is that Cobb walks away. He's also remarked on the centrality of creation imagery in the film and explicitly stated that "there's a relationship between the sand castle the kids are building on the beach in the beginning of the film and the buildings literally being eaten away by the subconscious and falling into the sea." Funny how he even specified the beginning of the film in that quote. No-one is post-rationalizing those words into his mouth.
Frankly, there's tremendous power to any interpretation that leads one independently to the same conclusions the director later makes, all the while explaining away what are inconsistencies under other readings (why Mal is bad, why the continual biblical references, why there is so much damn water in the dreams, etc. etc. etc.). The fact that Nolan is using fairly conventional symbolism (water = death/subconscious) is just icing on the cake.
We know Cobb doesn't need his totem by the end, because his rejection of Mal at the climax is an expression of faith. To understand the implicit alternative, look to the parallel heist sequence which opens the film. There we had a very different Cobb place his faith in the "reality" of Mal when he lowered himself out the window above a fatal fall. Nolan emphasizes that this is the wrong decision by showing us Cobb's immediate (biblical) fall, blasphemy and then betrayal and loss. Death destroys the world by water as foreshadowed in the parable that opens the film.
At the end of the film the logic of this sequence reverses. Cobb resists Mal's temptation to stay with her in limbo. He rejects her for the first time ever, telling Mal she is not "real" where even moments before he was expressing lingering doubts to Ariadne ("how can you know"). And whereas his lack of faith had previously led to his defeat, here his expression of it leads directly to Fischer's symbolic reconciliation with his father. And while the film presents another death sequence as required by Matthew 7.24, this is but prelude to a heaven sequence that breaks the endlessly circular logic of the dream world / penrose staircase. The rules are violated because they no longer apply: Cobb is free of the maze.
