Eques isn't literally manipulating any "plot" though, he's just destroying aspects of reality that were inscribed in a book. The Book of Traces holds the prior events and memories of things that occurred in the world, so naturally, destroying the vessel for those records would destroy the records as well; If you really want to bring other verses into this, we could easily say that verses like DMC, Touhou, or BlazBlue should all get plot hax because they have "books" that contain parts of reality. But they don't, because that massively stretches what plot manipulation even is.