### 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)
// IGNORED FOR NOW, they seem duplicated data compared to the shapes array
		} else if (what == "shape") {
		} else if (what == "shape_offset") {
		} else if (what == "shape_transform") {
		} else if (what == "shape_one_way") {
		} else if (what == "shape_one_way_margin") {
		}
		// IGNORED FOR NOW, maybe useless ?
		else if (what == "occluder_offset") {
			// Not
		} else if (what == "navigation_offset") {
		}
		*/
		} else if (what == "z_index") {
			ctd->z_index = p_value;
			
			_compatibility_conversion();
		} else {
			return false;
		}
	} else {
#endif 
		
		if (components.size() == 2 && components[0].begins_with("occlusion_layer_") && components[0].trim_prefix("occlusion_layer_").is_valid_int()) {
			
			int index = components[0].trim_prefix("occlusion_layer_").to_int();
			ERR_FAIL_COND_V(index < 0, false);
			if (components[1] == "light_mask") {
				ERR_FAIL_COND_V(p_value.get_type() != Variant::INT, false);
				while (index >= occlusion_layers.size()) {