### 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)

Vector<int> data;
	data.resize(pattern.size() * 3);
	int *w = data.ptrw();
	
	int idx = 0;
	for (const KeyValue<Vector2i, TileMapCell> &E : pattern) {
		uint8_t *ptr = (uint8_t *)&w[idx];
		encode_uint16((int16_t)(E.key.x), &ptr[0]);
		encode_uint16((int16_t)(E.key.y), &ptr[2]);
		encode_uint16(E.value.source_id, &ptr[4]);
		encode_uint16(E.value.coord_x, &ptr[6]);
		encode_uint16(E.value.coord_y, &ptr[8]);
		encode_uint16(E.value.alternative_tile, &ptr[10]);
		idx += 3;
	}
	return data;
}
void TileMapPattern::set_cell(const Vector2i &p_coords, int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) {