### 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)

overlapping_ratio = 0.5;
		} else if (tile_shape == TileSet::TILE_SHAPE_HEXAGON) {
			overlapping_ratio = 0.75;
		}
		ret.x /= overlapping_ratio;
	}
	
	if (tile_shape == TileSet::TILE_SHAPE_HALF_OFFSET_SQUARE || tile_shape == TileSet::TILE_SHAPE_HEXAGON || tile_shape == TileSet::TILE_SHAPE_ISOMETRIC) {
		
		
		if (tile_offset_axis == TileSet::TILE_OFFSET_AXIS_HORIZONTAL) {
			
			Vector2 raw_pos = ret;
			if (Math::posmod(Math::floor(ret.y), 2) ^ (tile_layout == TileSet::TILE_LAYOUT_STACKED_OFFSET)) {
				ret = Vector2(Math::floor(ret.x + 0.5) - 0.5, Math::floor(ret.y));
			} else {
				ret = ret.floor();
			}
			
			Vector2 in_tile_pos = raw_pos - ret;
			bool in_top_left_triangle = (in_tile_pos - Vector2(0.5, 0.0)).cross(Vector2(-0.5, 1.0 / overlapping_ratio - 1)) <= 0;
			bool in_top_right_triangle = (in_tile_pos - Vector2(0.5, 0.0)).cross(Vector2(0.5, 1.0 / overlapping_ratio - 1)) > 0;
			switch (tile_layout) {
				case TileSet::TILE_LAYOUT_STACKED:
					ret = ret.floor();
					if (in_top_left_triangle) {
						ret += Vector2i(Math::posmod(Math::floor(ret.y), 2) ? 0 : -1, -1);
					} else if (in_top_right_triangle) {
						ret += Vector2i(Math::posmod(Math::floor(ret.y), 2) ? 1 : 0, -1);
					}