TileMill takes raw datasources primarily - while in the future
it might be able to take tiles and essentially 're-tile' by
rendering over them, that's not its primary purpose.
As far as what you're trying to do - the tile analogy doesn't
work well in terms of GeoTiffs covering the planet (since you'll
usually be rendering at multiple resolutions, so a 256x256 tile
isn't very meaningful). The solution is indeed to combine GeoTIFFs
into much larger GeoTIFFs, which can be efficient internally, by