### 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)

PropertyInfo property_info;
	for (const KeyValue<Vector2i, TileAlternativesData> &E_tile : tiles) {
		List<PropertyInfo> tile_property_list;
		
		property_info = PropertyInfo(Variant::VECTOR2I, "size_in_atlas", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR);
		if (E_tile.value.size_in_atlas == Vector2i(1, 1)) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}