N.B. which I am sure you know already but your phrasing makes my "BUT BUT BUT" radar rise: The reason the movie feels so very much like Utena is because Hosoda worked pseudonymously on several significant chunks of that series, including being one of the section directors on the movie, and also it's not really Hosoda's first movie, he having multiple theatrical releases to his name for the Digimon franchise before this one. Unless we're not counting those as movies.
And to answer your question about the horror elements: given Hosoda's other work, I think I feel safe saying if it feels disorienting or unnerving then it's probably intentional on his part, as that same disaffected/unacknowledged unease is all over his Digimon work and his Utena segments, and though his work on One Piece Movie 6 allowed him to expunge most of it, it still bleeds into Summer Wars too, I think. And, more specifically to this movie, I believe the '70s novel it's based on was a romance/horror hybrid, and certainly the bits of the other adaptation I've seen of it bear that idea out. (There's been something like five adaptations of that novel since its publication. Talk about remake-heavy ...)
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And to answer your question about the horror elements: given Hosoda's other work, I think I feel safe saying if it feels disorienting or unnerving then it's probably intentional on his part, as that same disaffected/unacknowledged unease is all over his Digimon work and his Utena segments, and though his work on One Piece Movie 6 allowed him to expunge most of it, it still bleeds into Summer Wars too, I think. And, more specifically to this movie, I believe the '70s novel it's based on was a romance/horror hybrid, and certainly the bits of the other adaptation I've seen of it bear that idea out. (There's been something like five adaptations of that novel since its publication. Talk about remake-heavy ...)