### 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)

}
		} 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();
			ERR_FAIL_COND_V(index < 0, false);
			if (components[1] == "layers") {
				ERR_FAIL_COND_V(p_value.get_type() != Variant::INT, false);
				while (index >= navigation_layers.size()) {
					add_navigation_layer();
				}
				set_navigation_layer_layers(index, p_value);
				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();
			ERR_FAIL_COND_V(index < 0, false);
			if (components[1] == "name") {
				ERR_FAIL_COND_V(p_value.get_type() != Variant::STRING, false);
				while (index >= custom_data_layers.size()) {
					add_custom_data_layer();
				}
				set_custom_data_layer_name(index, p_value);
				return true;
			} else if (components[1] == "type") {
				ERR_FAIL_COND_V(p_value.get_type() != Variant::INT, false);
				while (index >= custom_data_layers.size()) {
					add_custom_data_layer();
				}
				set_custom_data_layer_type(index, Variant::Type(int(p_value)));