I’d suggest to allow tile size control on the properties of the layer, it would allow you to work with tiles of different sizes in one map, such as a main tile with 64x64 and a props tileset with 32x32.
Actually if you set the map to 64x64 when you use a 32x32 with it, it aligns each tile to the bottom left.
The idea looks better if you imagine making a ground and walls tileset with the size of 64x64 for bigger blocks in the map, and a 32x32 for smaller tileset for props such as small rocks, wall holes and this kind of stuffs