### 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)
if (layer_index >= physics.size()) {
				if (tile_set) {
					return false;
				} else {
					physics.resize(layer_index + 1);
				}
			}
			if (components[1] == "linear_velocity") {
				set_constant_linear_velocity(layer_index, p_value);
				return true;
			} else if (components[1] == "angular_velocity") {
				set_constant_angular_velocity(layer_index, p_value);
				return true;
			} else if (components[1] == "polygons_count") {
				if (p_value.get_type() != Variant::INT) {
					return false;
				}
				set_collision_polygons_count(layer_index, p_value);
				return true;
			}
		} else if (components.size() == 3 && components[1].begins_with("polygon_") && components[1].trim_prefix("polygon_").is_valid_int()) {
			int polygon_index = components[1].trim_prefix("polygon_").to_int();
			ERR_FAIL_COND_V(polygon_index < 0, false);
			if (components[2] == "points" || components[2] == "one_way" || components[2] == "one_way_margin") {
				if (layer_index >= physics.size()) {
					if (tile_set) {
						return false;
					} else {
						physics.resize(layer_index + 1);
					}