### 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 (source->has_tile(p_coords_from) && source->has_alternative_tile(p_coords_from, p_alternative_from)) {
			return from;
		}
	}
	
	if (alternative_level_proxies.has(from)) {
		return alternative_level_proxies[from].duplicate();
	}
	
	from.pop_back();
	if (coords_level_proxies.has(from)) {
		Array output = coords_level_proxies[from].duplicate();
		output.push_back(p_alternative_from);
		return output;
	}
	
	if (source_level_proxies.has(p_source_from)) {
		Array output;
		output.push_back(source_level_proxies[p_source_from]);
		output.push_back(p_coords_from);
		output.push_back(p_alternative_from);
		return output;
	}
	Array output;
	output.push_back(p_source_from);
	output.push_back(p_coords_from);
	output.push_back(p_alternative_from);
	return output;
}
void TileSet::cleanup_invalid_tile_proxies() {