The way I do it is after I place all the tiles with Tiled To Unity, I take a virtual grid over the world regardless of tile placement and combine the tiles based on that grid. An OBEY map can have up to 10,000 tiles... That is WAY too many draw calls (in a typical PC game you want about 1000 or less), so i combine them. But since each tile averages about 250 polys it's too much to combine them all into one (unity does not allow meshes with more than 65k verts), so I use the grid to turn 10,000 tiles into about 30 chunks/draw calls. Keep in mind they all use the same material and only have 1 material each, otherwise that would get split off into its own additional draw call.
You can avoid all this crap if you make a top down or isometric game!! lol