### 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)

TerrainConstraint terrain_bit_constraint = TerrainConstraint(tile_map_node, p_position, bit, terrain_pattern.get_terrain_peering_bit(bit));
				in_set_constraint_element = p_constraints.find(terrain_bit_constraint);
				if (in_set_constraint_element) {
					if (in_set_constraint_element->get().get_terrain() != terrain_bit_constraint.get_terrain()) {
						score += in_set_constraint_element->get().get_priority();
					}
				} else if (p_current_pattern.get_terrain_peering_bit(bit) != terrain_pattern.get_terrain_peering_bit(bit)) {
					invalid_pattern = true; 
					break;
				}
			}
		}
		if (invalid_pattern) {
			continue;
		}
		terrain_pattern_score[terrain_pattern] = score;
	}
	
	TileSet::TerrainsPattern min_score_pattern = p_current_pattern;
	int min_score = INT32_MAX;
	for (KeyValue<TileSet::TerrainsPattern, int> E : terrain_pattern_score) {
		if (E.value < min_score) {
			min_score_pattern = E.key;
			min_score = E.value;
		}
	}
	return min_score_pattern;
}
RBSet<TerrainConstraint> TileMapLayer::_get_terrain_constraints_from_added_pattern(const Vector2i &p_position, int p_terrain_set, TileSet::TerrainsPattern p_terrains_pattern) const {