### 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)

ERR_FAIL_INDEX_V(p_index, source_ids.size(), TileSet::INVALID_SOURCE);
	return source_ids[p_index];
}
void TileSet::set_uv_clipping(bool p_uv_clipping) {
	if (uv_clipping == p_uv_clipping) {
		return;
	}
	uv_clipping = p_uv_clipping;
	emit_changed();
}
bool TileSet::is_uv_clipping() const {
	return uv_clipping;
};
int TileSet::get_occlusion_layers_count() const {
	return occlusion_layers.size();
};
void TileSet::add_occlusion_layer(int p_index) {
	if (p_index < 0) {
		p_index = occlusion_layers.size();
	}
	ERR_FAIL_INDEX(p_index, occlusion_layers.size() + 1);
	occlusion_layers.insert(p_index, OcclusionLayer());
	for (KeyValue<int, Ref<TileSetSource>> source : sources) {
		source.value->add_occlusion_layer(p_index);
	}
	notify_property_list_changed();
	emit_changed();
}
void TileSet::move_occlusion_layer(int p_from_index, int p_to_pos) {