### 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)

ERR_FAIL_COND_V(p_terrain_set < 0 || p_terrain_set >= get_terrain_sets_count(), Vector<Point2>());
	TileSet::TerrainMode terrain_mode = get_terrain_set_mode(p_terrain_set);
	if (tile_shape == TileSet::TILE_SHAPE_SQUARE) {
		if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES) {
			return _get_square_corner_or_side_terrain_peering_bit_polygon(tile_size, p_bit);
		} else if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
			return _get_square_corner_terrain_peering_bit_polygon(tile_size, p_bit);
		} else { 
			return _get_square_side_terrain_peering_bit_polygon(tile_size, p_bit);
		}
	} else if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES) {
			return _get_isometric_corner_or_side_terrain_peering_bit_polygon(tile_size, p_bit);
		} else if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
			return _get_isometric_corner_terrain_peering_bit_polygon(tile_size, p_bit);
		} else { 
			return _get_isometric_side_terrain_peering_bit_polygon(tile_size, p_bit);
		}
	} else {
		float overlap = 0.0;
		switch (tile_shape) {
			case TileSet::TILE_SHAPE_HEXAGON: