Ahh ok, that should work, I can just loop through them all, and set the renderOrder myself from Bottom-Right, doh!
Definitely would be nice to have support for animations baked into the Toolkit. Or an option to force everything to be "sprites" so we don't have to manually create prefabs just to force TileMap to not batch them.
You could even add a "Exclude from Batch" or or "Render as Sprite" checkbox, on the Data setting for each tile. Then we'd just need to highlight the tile, check the checkbox and then run a simple loop to assign order position.