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I don't think it's the albeit that's the issue - in the first half of the sentence the subject is singular and in the second half it is plural.
How about Jake, like Huckleberry Finn and Harry Potter, must make his own way in the world, even thought he inhabits a very different fictional setting from them.
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How about
Jake, like Huckleberry Finn and Harry Potter, must make his own way in the world, even thought he inhabits a very different fictional setting from them.