### 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)

Vector2 unit = Vector2(p_size) / 6.0;
	Vector<Vector2> polygon;
	switch (p_bit) {
		case TileSet::CELL_NEIGHBOR_RIGHT_CORNER:
			polygon.push_back(Vector2(1, 0) * unit);
			polygon.push_back(Vector2(2, -1) * unit);
			polygon.push_back(Vector2(3, 0) * unit);
			polygon.push_back(Vector2(2, 1) * unit);
			break;
		case TileSet::CELL_NEIGHBOR_BOTTOM_RIGHT_SIDE:
			polygon.push_back(Vector2(0, 1) * unit);
			polygon.push_back(Vector2(1, 2) * unit);
			polygon.push_back(Vector2(2, 1) * unit);
			polygon.push_back(Vector2(1, 0) * unit);
			break;
		case TileSet::CELL_NEIGHBOR_BOTTOM_CORNER:
			polygon.push_back(Vector2(0, 1) * unit);
			polygon.push_back(Vector2(-1, 2) * unit);
			polygon.push_back(Vector2(0, 3) * unit);
			polygon.push_back(Vector2(1, 2) * unit);
			break;
		case TileSet::CELL_NEIGHBOR_BOTTOM_LEFT_SIDE:
			polygon.push_back(Vector2(0, 1) * unit);
			polygon.push_back(Vector2(-1, 2) * unit);
			polygon.push_back(Vector2(-2, 1) * unit);
			polygon.push_back(Vector2(-1, 0) * unit);
			break;