### 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)

overlap = 0.25;
				break;
			case TileSet::TILE_SHAPE_HALF_OFFSET_SQUARE:
				overlap = 0.0;
				break;
			default:
				break;
		}
		if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS_AND_SIDES) {
			return _get_half_offset_corner_or_side_terrain_peering_bit_polygon(tile_size, overlap, tile_offset_axis, p_bit);
		} else if (terrain_mode == TileSet::TERRAIN_MODE_MATCH_CORNERS) {
			return _get_half_offset_corner_terrain_peering_bit_polygon(tile_size, overlap, tile_offset_axis, p_bit);
		} else { 
			return _get_half_offset_side_terrain_peering_bit_polygon(tile_size, overlap, tile_offset_axis, p_bit);
		}
	}
}
#define TERRAIN_ALPHA 0.6
void TileSet::draw_terrains(CanvasItem *p_canvas_item, Transform2D p_transform, const TileData *p_tile_data) {
	ERR_FAIL_NULL(p_tile_data);
	if (terrain_bits_meshes_dirty) {
		
		terrain_peering_bits_meshes.clear();
		for (int terrain_mode_index = 0; terrain_mode_index < 3; terrain_mode_index++) {
			TerrainMode terrain_mode = TerrainMode(terrain_mode_index);
			
			Vector<Vector2> polygon;
			if (tile_shape == TileSet::TILE_SHAPE_SQUARE) {
				polygon = _get_square_terrain_polygon(tile_size);
			} else if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {