Currently "Collection of Images" Tilesets are already supported, but only using individual images.
However it's possible to use image collections and then pack them in an atlas, effectively indexing tile images by name rather than GID and offset within texture.
Details here:
http://forum.mapeditor.org/t/best-way-to-use-tiled-with-texture-packer-custom-game-engine/361
This should be straightforward except for the tile texture caching and lookup algorithms, they may need a different "mode" and the use of texture rects would not be necessary.
Estimate: 1-3 days.