### Godot version

4.01

### System information

Windows 10

### Issue description

It seems a tiles Custom Data is cleared/not set when "Local to Scene" is enabled for the TileMap in the Resource section. At least the custom data isn't set by the time of the _ready function in the script attached to the TileMap.

### Steps to reproduce

create TileMap and tileset with custom data and attached script. in _ready method attempt to read custom data from a used cell. 

In Attached project run it. It will print_debug if it found custom data or not. "Local to Scene" is enabled so it will not find the custom data.

### Minimal reproduction project

[TileMapCustomDataLocalBugReproduce.zip](https://github.com/godotengine/godot/files/11470771/TileMapCustomDataLocalBugReproduce.zip)

}
			if (components[2] == "name") {
				r_ret = get_terrain_name(terrain_set_index, terrain_index);
				return true;
			} else if (components[2] == "color") {
				r_ret = get_terrain_color(terrain_set_index, terrain_index);
				return true;
			}
		}
	} else if (components.size() == 2 && components[0].begins_with("navigation_layer_") && components[0].trim_prefix("navigation_layer_").is_valid_int()) {
		
		int index = components[0].trim_prefix("navigation_layer_").to_int();
		if (index < 0 || index >= navigation_layers.size()) {
			return false;
		}
		if (components[1] == "layers") {
			r_ret = get_navigation_layer_layers(index);
			return true;
		}
	} else if (components.size() == 2 && components[0].begins_with("custom_data_layer_") && components[0].trim_prefix("custom_data_layer_").is_valid_int()) {
		
		int index = components[0].trim_prefix("custom_data_layer_").to_int();
		if (index < 0 || index >= custom_data_layers.size()) {
			return false;
		}
		if (components[1] == "name") {
			r_ret = get_custom_data_layer_name(index);
			return true;
		} else if (components[1] == "type") {
			r_ret = get_custom_data_layer_type(index);