I agree the Tiled API could use some improvement when it comes to querying in this way.
If it helps have a read about the TMX map format. That should at least help you understand why it’s currently modeled this way.
Basically to figure out what tile is in a layer you need to lookup what tileset it comes from.
Next time I’m making improvements to the Tiled code I’ll take your feedback into account and implement a bunch of helper methods for this kind of querying.