I think Inception might have the same "problem" that Blade Runner has. Although, knowing how much a fan of Blade Runner Nolan is, perhaps it's on purpose.
Blade Runner is ostensibly about loss of humanity, and that Roy Batty, a replicant, can feel and love life more than a human. But if the "twist" of it all is that Deckerd is a replicant himself, it kind of robs the movie of thematic weight for a satirically dark twist.
I agree with you on that, and my takeaway from Blade Runner has always been that Deckard is human, but all the clues that he was a replicant are there just to underscore how human replicants were. It's not just that the robots were starting to think they were human, the humans were starting to wonder if they were robots.
So mapping that to Inception, it means Cobb had woken up, but he'd gotten so lost between dream and reality that it almost couldn't matter. He ended up with the same outlook Mal had before he planted the idea in her head that she was dreaming, where she wouldn't and couldn't care what was objectively real anymore, and all she could appreciate was the reality she was in at that moment. He was just lucky enough to end up on the correct side of the veil.