### 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)

tile_property_list.push_back(property_info);
		
		property_info = PropertyInfo(Variant::INT, "next_alternative_id", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR);
		if (E_tile.value.next_alternative_id == 1) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}
		tile_property_list.push_back(property_info);
		
		property_info = PropertyInfo(Variant::INT, "animation_columns", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR);
		if (E_tile.value.animation_columns == 0) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}
		tile_property_list.push_back(property_info);
		
		property_info = PropertyInfo(Variant::INT, "animation_separation", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR);
		if (E_tile.value.animation_separation == Vector2i()) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}
		tile_property_list.push_back(property_info);
		
		property_info = PropertyInfo(Variant::FLOAT, "animation_speed", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NO_EDITOR);
		if (E_tile.value.animation_speed == 1.0) {
			property_info.usage ^= PROPERTY_USAGE_STORAGE;
		}
		tile_property_list.push_back(property_info);
		
		tile_property_list.push_back(PropertyInfo(Variant::INT, "animation_frames_count", PROPERTY_HINT_NONE, "", PROPERTY_USAGE_NONE));
		
		bool store_durations = tiles[E_tile.key].animation_frames_durations.size() >= 2;
		for (int i = 0; i < (int)tiles[E_tile.key].animation_frames_durations.size(); i++) {