### Godot version

4.2.dev3.official[013e8e3af]

### System information

Godot v4.2.dev3 - Arch Linux #1 SMP PREEMPT_DYNAMIC Fri, 11 Aug 2023 11:03:36 +0000 - X11 - GLES3 (Compatibility) - NVIDIA GeForce RTX 2060 (nvidia; 535.98) - Intel(R) Core(TM) i7-10875H CPU @ 2.30GHz (16 Threads)

### Issue description

`TileMap.get_used_cells_by_id()` seems not work as expected.
It seems that this method will return the same result as "TileMap.get_used_cells()" since Godot 4.2dev2.
The arguments  (`source_id: int`, `atlas_coords: Vector2i`, `alternative_tile: int`) of `get_used_cells_by_id()` seems not make the filter working as expected.  It would only return the same result as `get_used_cells()`, contains all the tiles on the layer.

### Steps to reproduce

1. create a tilemap scene
2. attach a tileset, that contains  at least 2 tiles , paint some tiles.
3. calls Tilemap.get_used_cells_by_id(layer, source_id, atlas_coords,alternative_tile)
4. run it

### Minimal reproduction project

run tile_map.tscn by Godot4dev3 (or custom build)
[tilemap_debug.zip](https://github.com/godotengine/godot/files/12369631/tilemap_debug.zip)

if (!source->has_tile(c.get_atlas_coords()) || !source->has_alternative_tile(c.get_atlas_coords(), c.alternative_tile)) {
				continue;
			}
			TileSetAtlasSource *atlas_source = Object::cast_to<TileSetAtlasSource>(source);
			if (atlas_source) {
				Vector2i grid_size = atlas_source->get_atlas_grid_size();
				if (!atlas_source->get_runtime_texture().is_valid() || c.get_atlas_coords().x >= grid_size.x || c.get_atlas_coords().y >= grid_size.y) {
					
					Array to_hash;
					to_hash.push_back(c.source_id);
					to_hash.push_back(c.get_atlas_coords());
					to_hash.push_back(c.alternative_tile);
					uint32_t hash = RandomPCG(to_hash.hash()).rand();
					Color color;
					color = color.from_hsv(
							(float)((hash >> 24) & 0xFF) / 256.0,
							Math::lerp(0.5, 1.0, (float)((hash >> 16) & 0xFF) / 256.0),
							Math::lerp(0.5, 1.0, (float)((hash >> 8) & 0xFF) / 256.0),
							0.8);
					
					Transform2D cell_to_quadrant;
					cell_to_quadrant.set_origin(tile_map_node->map_to_local(E_cell) - quadrant_pos);
					rs->canvas_item_add_set_transform(p_quadrant->debug_canvas_item, cell_to_quadrant);
					rs->canvas_item_add_circle(p_quadrant->debug_canvas_item, Vector2(), MIN(tile_set->get_tile_size().x, tile_set->get_tile_size().y) / 4.0, color);
				}
			}
		}
	}
}
void TileMapLayer::_physics_update_dirty_quadrants(SelfList<TileMapQuadrant>::List &r_dirty_quadrant_list) {