### 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<Vector2> point_list = {
		Vector2(3, 3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(0, 3),
		Vector2(-3, 3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(-3, -3.0 * (1.0 - p_overlap * 2.0)),
		Vector2(0, -3),
		Vector2(3, -3.0 * (1.0 - p_overlap * 2.0))
	};
	Vector2 unit = Vector2(p_size) / 6.0;
	Vector<Vector2> polygon;
	if (p_offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
		for (int i = 0; i < point_list.size(); i++) {
			point_list.write[i] = point_list[i] * unit;
		}
		switch (p_bit) {
			case TileSet::CELL_NEIGHBOR_RIGHT_SIDE:
				polygon.push_back(point_list[5]);
				polygon.push_back(point_list[0]);
				break;
			case TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE:
				polygon.push_back(point_list[0]);
				polygon.push_back(point_list[1]);