Different sprites are on separate layers. Why???

How do I add sprite variation in the same layer? Why is it rendered separately? Are tiles not packed and can’t be rendered in one pass? Do I have to pack them? I think I did, and I think it doesn’t change anything.

NOTE that it’s not a tint, but a separate sprite. Tiles with the same sprite and different tint are rendered in one layer.

And lastly, to be clear I want these tiles to be on the same player, but currently, the yellowish ones are all on top.

3655999--299134--upload_2018-9-9_14-13-24.png

Okay, I packed them again, and now they are in one layer IN RUNTIME (in play mode), but not in edit mode… Seems like Atlas and Tilemap are not cooperating.