### Godot version

4.2 beta 2

### System information

Pop Os 22.04 lts 12th Gen Intel® Core™ i7-12700H × 20 NVIDIA RTX A2000 8GB 32.0  ram. Tested on Forward+ and Mobile

### Issue description

When painting a tile that is rotated or flipped, it looses its physics layer as demonstrated in this video:  

https://github.com/godotengine/godot/assets/33091666/c10f7325-838f-4112-b90d-0c3d9797d08f

Even though in the video I showed this only happening with one of the tiles, it happens with both of them as long as you rotate or flip it. 

### Steps to reproduce

1. Create a tilemap and a tileset
2. Create a physics layer and set collision_visibility_mode to force show. 
3. Assign just created physics layer to tiles
4. Paint the tiles and use rotate or flip tool. 

### Minimal reproduction project

[TileTest.zip](https://github.com/godotengine/godot/files/13067412/TileTest.zip)
}
					p.pop_front();
				}
			} else if (what == "priority_map") {
				Array p = p_value;
				Vector3 val;
				Vector2 v;
				int priority;
				while (p.size() > 0) {
					val = p[0];
					if (val.z > 1) {
						v.x = val.x;
						v.y = val.y;
						priority = (int)val.z;
						ctd->autotile_priority_map.insert(v, priority);
					}
					p.pop_front();
				}
			} else if (what == "z_index_map") {
				Array p = p_value;
				Vector3 val;
				Vector2 v;
				int z_index;
				while (p.size() > 0) {
					val = p[0];
					if (val.z != 0) {
						v.x = val.x;
						v.y = val.y;
						z_index = (int)val.z;
						ctd->autotile_z_index_map.insert(v, z_index);