It would be a neat feature to support different tile sizes per layer. At least I have the need for it. 
Looking at the TMX format there seems to be attributes in the layer tag supporting it, but it may just be derived from the map tag?
Of course, to make it easier the layer tile size must be an even divided or multiplied by 2 from the map size.
I believe that’s actually a tileset thing rather than layers. Layers provide the grid (same as the map) but you can still have individual tiles larger than the grid.
So for instance you could use two tilesets on the same layer whose grid size is 32x32. And your tilesets are 32x32 and 64x64. When you draw tiles from the 64 tileset you’d just have to be careful to only place them every other grid coordinate - but that’s self-explanatory.
There are indeed situations in which different tile sizes per layer would be useful, and it’s something I’d like to support eventually. It is covered by the following issue on github:
https://github.com/bjorn/tiled/issues/149
Of course, if you want to help me get around to more stuff, please consider supporting me on Patreon so that I could eventually work two full days a week on Tiled!