I don’t know about different tilesizes per tilelayer. But you could always add in the second and third layer tiles as objects in an object layer. Then you’re not stuck to a grid. Would be a cool feature to have different tilesizes, though.
Right, I think in this particular case, you’re not actually looking for layers with different tile sizes, since it would be very hard to place those tiles the way that you want (since the sizes are not even multiples of each other). So like @Tipsi suggested you’ll probably want to use object layers instead, and just use a tile layer for the terrain.
In general though, there have been a lot of requests for supporting tile size per tile layer and of course this make sense in some situations. It is unfortunately hard to support due to the handling of the selected tile area and the multi-layer editing, both of which currently assume a map-global tile grid. This feature is covered by the following issue: