### 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)

ClassDB::bind_method(D_METHOD("get_tile_size_in_atlas", "atlas_coords"), &TileSetAtlasSource::get_tile_size_in_atlas);
	ClassDB::bind_method(D_METHOD("has_room_for_tile", "atlas_coords", "size", "animation_columns", "animation_separation", "frames_count", "ignored_tile"), &TileSetAtlasSource::has_room_for_tile, DEFVAL(INVALID_ATLAS_COORDS));
	ClassDB::bind_method(D_METHOD("get_tiles_to_be_removed_on_change", "texture", "margins", "separation", "texture_region_size"), &TileSetAtlasSource::get_tiles_to_be_removed_on_change);
	ClassDB::bind_method(D_METHOD("get_tile_at_coords", "atlas_coords"), &TileSetAtlasSource::get_tile_at_coords);
	ClassDB::bind_method(D_METHOD("set_tile_animation_columns", "atlas_coords", "frame_columns"), &TileSetAtlasSource::set_tile_animation_columns);
	ClassDB::bind_method(D_METHOD("get_tile_animation_columns", "atlas_coords"), &TileSetAtlasSource::get_tile_animation_columns);
	ClassDB::bind_method(D_METHOD("set_tile_animation_separation", "atlas_coords", "separation"), &TileSetAtlasSource::set_tile_animation_separation);
	ClassDB::bind_method(D_METHOD("get_tile_animation_separation", "atlas_coords"), &TileSetAtlasSource::get_tile_animation_separation);
	ClassDB::bind_method(D_METHOD("set_tile_animation_speed", "atlas_coords", "speed"), &TileSetAtlasSource::set_tile_animation_speed);
	ClassDB::bind_method(D_METHOD("get_tile_animation_speed", "atlas_coords"), &TileSetAtlasSource::get_tile_animation_speed);
	ClassDB::bind_method(D_METHOD("set_tile_animation_frames_count", "atlas_coords", "frames_count"), &TileSetAtlasSource::set_tile_animation_frames_count);
	ClassDB::bind_method(D_METHOD("get_tile_animation_frames_count", "atlas_coords"), &TileSetAtlasSource::get_tile_animation_frames_count);
	ClassDB::bind_method(D_METHOD("set_tile_animation_frame_duration", "atlas_coords", "frame_index", "duration"), &TileSetAtlasSource::set_tile_animation_frame_duration);
	ClassDB::bind_method(D_METHOD("get_tile_animation_frame_duration", "atlas_coords", "frame_index"), &TileSetAtlasSource::get_tile_animation_frame_duration);
	ClassDB::bind_method(D_METHOD("get_tile_animation_total_duration", "atlas_coords"), &TileSetAtlasSource::get_tile_animation_total_duration);
	
	ClassDB::bind_method(D_METHOD("create_alternative_tile", "atlas_coords", "alternative_id_override"), &TileSetAtlasSource::create_alternative_tile, DEFVAL(INVALID_TILE_ALTERNATIVE));
	ClassDB::bind_method(D_METHOD("remove_alternative_tile", "atlas_coords", "alternative_tile"), &TileSetAtlasSource::remove_alternative_tile);
	ClassDB::bind_method(D_METHOD("set_alternative_tile_id", "atlas_coords", "alternative_tile", "new_id"), &TileSetAtlasSource::set_alternative_tile_id);
	ClassDB::bind_method(D_METHOD("get_next_alternative_tile_id", "atlas_coords"), &TileSetAtlasSource::get_next_alternative_tile_id);
	ClassDB::bind_method(D_METHOD("get_tile_data", "atlas_coords", "alternative_tile"), &TileSetAtlasSource::get_tile_data);
	
	ClassDB::bind_method(D_METHOD("get_atlas_grid_size"), &TileSetAtlasSource::get_atlas_grid_size);
	ClassDB::bind_method(D_METHOD("get_tile_texture_region", "atlas_coords", "frame"), &TileSetAtlasSource::get_tile_texture_region, DEFVAL(0));
	
	ClassDB::bind_method(D_METHOD("_update_padded_texture"), &TileSetAtlasSource::_update_padded_texture);
	ClassDB::bind_method(D_METHOD("get_runtime_texture"), &TileSetAtlasSource::get_runtime_texture);
	ClassDB::bind_method(D_METHOD("get_runtime_tile_texture_region", "atlas_coords", "frame"), &TileSetAtlasSource::get_runtime_tile_texture_region);
}
TileSetAtlasSource::~TileSetAtlasSource() {