### 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)

set_navigation_polygon(layer_index, polygon);
			return true;
		}
	} else if (components.size() == 2 && components[0] == "terrains_peering_bit") {
		
		for (int i = 0; i < TileSet::CELL_NEIGHBOR_MAX; i++) {
			TileSet::CellNeighbor bit = TileSet::CellNeighbor(i);
			if (components[1] == TileSet::CELL_NEIGHBOR_ENUM_TO_TEXT[i]) {
				set_terrain_peering_bit(bit, p_value);
				return true;
			}
		}
		return false;
	} else if (components.size() == 1 && components[0].begins_with("custom_data_") && components[0].trim_prefix("custom_data_").is_valid_int()) {
		
		int layer_index = components[0].trim_prefix("custom_data_").to_int();
		ERR_FAIL_COND_V(layer_index < 0, false);
		if (layer_index >= custom_data.size()) {
			if (tile_set) {
				return false;
			} else {
				custom_data.resize(layer_index + 1);
			}
		}
		set_custom_data_by_layer_id(layer_index, p_value);
		return true;
	}
	return false;
}
bool TileData::_get(const StringName &p_name, Variant &r_ret) const {