Thanks for the plentiful examples! I definitely see what you mean. SMW's use of 8x8 tiles to form its larger 16x16 tiles definitely gives a lot more flexibility in design. That's something I definitely want as well.
Currently you can very much combat the issue, albeit a little awkwardly. If you build your map in the editor, then export it as a PNG and edit it in an image editing software, then re-import it as larger chunks and re-build that in the game, you can have a map that looks however you want. There is a guide on it here
and it was first used in this map
to subtly have more tile colours than ought to be possible.
Though even with half-tiling, there's some things that are always gonna be a pain, I suppose. It can for example look really awkward if islands are slanted towards the camera, that is to say if a plateau doesn't have the same height of wall tiles around all its edges facing the screen, like in your second image. Or if the player gets off a plateau westwards/eastwards/northwards by means of anything other than a bridge, like in your third image, because he'd be technically jumping downwards and northwards. I wonder if there is a way to make these things more intuitive as well.