I don't think adamantyr is using Magellan, but when I have been working on projects that needed lots of tiles (Dungeons of Asgard), what I needed was to have them in the tile set so they could be exported (even though the 256 limit was exceeded). Sometimes I would also have liked to have different tile sets for different maps, but that can be dealt with by having multiple files.
I don't use Magellan for my game, no. That's partly though because I built my tools for map creation on the TI awhile back. And I have other metadata (lighting and elevation) that is stored along with the tiles, something that's beyond Magellan's boundaries.