I'm glad you brought this up, Phantom, because I actually didn't notice that Mana had transposed anything to accommodate Seth's different vocal range. I just did a side-by-side comparison though, and the only track that I'm hearing a key change in is Solitude, which makes sense because so much of that song is originally sung in the upper register and in falsetto. I would have thought that Dialogue Symphonie would have been among the songs Mana transposed, because it also has some falsetto that Seth impressively but barely pulls off--but alas, it is in the same exact key as the original.
I was skeptical that Monophobia would pose any difficulty for Seth to sing in the original key, because it has no falsetto like Dialogue Symphonie does (yet he sings DS fine in its original key). But the "Break a spell" parts of Monophobia are in about the same range as the higher parts of Solitude (minus the falsetto), so it's plausible that if Mana wasn't satisfied with Seth's singing in Solitude's original key maybe he wasn't with Seth's singing in Monophobia's original key either.
However, even in the original track there is one iteration of the "break a spell" section where Juka sits it out and the singing is left to the "choir". If this section were the only problematic one for Seth to sing, why not just let him sit it out every time?
So I'm still skeptical that this is really the reason Monophobia wasn't included, but it's a sensible theory.
And Helkär is right, that it was supposed to be based on fan votes. If Monophobia were highly requested, why wouldn't Mana have tried to come up with a solution like the simple one I came up with?
My original theory for why it was left out is that it's such a personal, sentimental song, maybe Mana didn't feel that it was appropriate for reinterpretation/tinkering, or was afraid that reinterpreting it would diminish it. I think that's a plausible theory too.
EDIT: Another problem with your theory, Phantom, is that Vestige seems to get as high-pitched as Monophobia. Seth is kind of straining to pull it off, but he does it.