I think the whole overlaying maps should be loosely interpreted, not literal like many people are doing:
example: OMGZ! Kakariko Village in TP is 2.5 degrees off of the coordinates of OOT! Some cataclysmic event moved it.
The above is an exaggeration of what people say, of course. But seriously, I think Miyamoto places the villages and other important locations roughly where they ought to be, not spot on. If he did, then every Zelda game would, by necessity, have to be the same dimensions map-wise every single time, and that, well, gets old. If the games are to grow, so are the maps.
The slightly off placements of certain locations (or altogether different locations) are placed there not to confuse the timeline or because of cataclysmic events or whatnot, but simply, to expand the world that us, as gamers, can navigate. At most, I'd say each game produced reveals to us more of what the world of Hyrule really IS, rather than story-driven changes. Each following game produced reveals features and details that were not doable before because of tech limitations. Simply put, the world of Hyrule is expanding because technology allows Miyamoto to do that, and every time that happens he "paints" us a better picture of what he imagines Hyrule to be.