### 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)

}
		ret.y *= overlapping_ratio;
	} else { 
		if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
			overlapping_ratio = 0.5;
		} else if (tile_shape == TileSet::TILE_SHAPE_HEXAGON) {
			overlapping_ratio = 0.75;
		}
		ret.x *= overlapping_ratio;
	}
	return (ret + Vector2(0.5, 0.5)) * tile_set->get_tile_size();
}
Vector2i TileMap::local_to_map(const Vector2 &p_local_position) const {
	ERR_FAIL_COND_V(!tile_set.is_valid(), Vector2i());
	Vector2 ret = p_local_position;
	ret /= tile_set->get_tile_size();
	TileSet::TileShape tile_shape = tile_set->get_tile_shape();
	TileSet::TileOffsetAxis tile_offset_axis = tile_set->get_tile_offset_axis();
	TileSet::TileLayout tile_layout = tile_set->get_tile_layout();
	
	double overlapping_ratio = 1.0;
	if (tile_offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
		if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
			overlapping_ratio = 0.5;
		} else if (tile_shape == TileSet::TILE_SHAPE_HEXAGON) {
			overlapping_ratio = 0.75;
		}
		ret.y /= overlapping_ratio;
	} else { 
		if (tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {