If I have correctly recreated your situation.

Solving:

You change the atlas so that it is a single tile, for example 2 by 3.

Result:

Это решение наиболее правильное.

Alternative (not the best method)

You select coloring in the tile set and specify the Z-index in the properties.

If I have correctly recreated your situation.

Solving:

You change the atlas so that it is a single tile, for example 2 by 3.

Result:

The above solution is the most correct. But I also have an alternative below.

Alternative (not the best method)

You select coloring in the tile set and specify the Z-index in the properties.

If I have correctly recreated your situation.

Solving:

You change the atlas so that it is a single tile, for example 2 by 3.

Result:

If I have correctly recreated your situation.

Solving:

You change the atlas so that it is a single tile, for example 2 by 3.

Result:

Это решение наиболее правильное.

Alternative (not the best method)

You select coloring in the tile set and specify the Z-index in the properties.