I thought it was clear from some exposition somewhere that the worlds were recreated again and split for a time, destined to eventually merge again, but Noah retained something from his connection to Mio that allowed him to find his way to Alrest. He disappears when the birds on the screen obscure him from vision in the final scene. If the worlds were merged, it wouldn't have been portrayed as being spirited away.
Spiriting him away is itself pretty ambiguous. He was in a large crowd and could just have disappeared into that, maybe he poofed to another world, maybe the worlds merged and he ended up poofing to where he was supposed to be in the merged world, maybe he was always an anomaly that came into existence for the sake of resolving the events of the game (hence he didn't freeze when everything else did) and was subsequently erased once that purpose was filled... Like a lot of the game, it's left pretty open, with little to go on except a vague "he probably didn't have to live without Mio so don't be sad."
Either way, the ambiguous ending works. I'd love to see a conclusive happy ending for everyone because I just loved these characters and their interactions so much, but I'm not surprised the game didn't give that based on how central the theme of "you're not going to know what the future holds and that's okay" was to the overall story.
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