### 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)

TILEMAP_CALL_FOR_LAYER_V(p_layer, TileSetSource::INVALID_TILE_ALTERNATIVE, get_cell_alternative_tile, p_coords, p_use_proxies);
}
TileData *TileMap::get_cell_tile_data(int p_layer, const Vector2i &p_coords, bool p_use_proxies) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, nullptr, get_cell_tile_data, p_coords, p_use_proxies);
}
Ref<TileMapPattern> TileMap::get_pattern(int p_layer, TypedArray<Vector2i> p_coords_array) {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, Ref<TileMapPattern>(), get_pattern, p_coords_array);
}
Vector2i TileMap::map_pattern(const Vector2i &p_position_in_tilemap, const Vector2i &p_coords_in_pattern, Ref<TileMapPattern> p_pattern) {
	ERR_FAIL_COND_V(p_pattern.is_null(), Vector2i());
	ERR_FAIL_COND_V(!p_pattern->has_cell(p_coords_in_pattern), Vector2i());
	Vector2i output = p_position_in_tilemap + p_coords_in_pattern;
	if (tile_set->get_tile_shape() != TileSet::TILE_SHAPE_SQUARE) {
		if (tile_set->get_tile_layout() == TileSet::TILE_LAYOUT_STACKED) {
			if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL && bool(p_position_in_tilemap.y % 2) && bool(p_coords_in_pattern.y % 2)) {
				output.x += 1;
			} else if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_VERTICAL && bool(p_position_in_tilemap.x % 2) && bool(p_coords_in_pattern.x % 2)) {
				output.y += 1;
			}
		} else if (tile_set->get_tile_layout() == TileSet::TILE_LAYOUT_STACKED_OFFSET) {
			if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_HORIZONTAL && bool(p_position_in_tilemap.y % 2) && bool(p_coords_in_pattern.y % 2)) {
				output.x -= 1;
			} else if (tile_set->get_tile_offset_axis() == TileSet::TILE_OFFSET_AXIS_VERTICAL && bool(p_position_in_tilemap.x % 2) && bool(p_coords_in_pattern.x % 2)) {
				output.y -= 1;
			}
		}
	}
	return output;
}
void TileMap::set_pattern(int p_layer, const Vector2i &p_position, const Ref<TileMapPattern> p_pattern) {