### 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_COND_V(!scenes.has(p_id), Ref<PackedScene>());
	return scenes[p_id].scene;
}
void TileSetScenesCollectionSource::set_scene_tile_display_placeholder(int p_id, bool p_display_placeholder) {
	ERR_FAIL_COND(!scenes.has(p_id));
	scenes[p_id].display_placeholder = p_display_placeholder;
	emit_signal(SNAME("changed"));
}
bool TileSetScenesCollectionSource::get_scene_tile_display_placeholder(int p_id) const {
	ERR_FAIL_COND_V(!scenes.has(p_id), false);
	return scenes[p_id].display_placeholder;
}
void TileSetScenesCollectionSource::remove_scene_tile(int p_id) {