### 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(p_layer, set_pattern, p_position, p_pattern);
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMap::terrain_fill_constraints(int p_layer, const Vector<Vector2i> &p_to_replace, int p_terrain_set, const RBSet<TerrainConstraint> &p_constraints) {
	HashMap<Vector2i, TileSet::TerrainsPattern> err_value;
	TILEMAP_CALL_FOR_LAYER_V(p_layer, err_value, terrain_fill_constraints, p_to_replace, p_terrain_set, p_constraints);
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMap::terrain_fill_connect(int p_layer, const Vector<Vector2i> &p_coords_array, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	HashMap<Vector2i, TileSet::TerrainsPattern> err_value;
	TILEMAP_CALL_FOR_LAYER_V(p_layer, err_value, terrain_fill_connect, p_coords_array, p_terrain_set, p_terrain, p_ignore_empty_terrains);
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMap::terrain_fill_path(int p_layer, const Vector<Vector2i> &p_coords_array, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	HashMap<Vector2i, TileSet::TerrainsPattern> err_value;
	TILEMAP_CALL_FOR_LAYER_V(p_layer, err_value, terrain_fill_path, p_coords_array, p_terrain_set, p_terrain, p_ignore_empty_terrains);
}
HashMap<Vector2i, TileSet::TerrainsPattern> TileMap::terrain_fill_pattern(int p_layer, const Vector<Vector2i> &p_coords_array, int p_terrain_set, TileSet::TerrainsPattern p_terrains_pattern, bool p_ignore_empty_terrains) {
	HashMap<Vector2i, TileSet::TerrainsPattern> err_value;
	TILEMAP_CALL_FOR_LAYER_V(p_layer, err_value, terrain_fill_pattern, p_coords_array, p_terrain_set, p_terrains_pattern, p_ignore_empty_terrains);
}
void TileMap::set_cells_terrain_connect(int p_layer, TypedArray<Vector2i> p_cells, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_cells_terrain_connect, p_cells, p_terrain_set, p_terrain, p_ignore_empty_terrains);
}
void TileMap::set_cells_terrain_path(int p_layer, TypedArray<Vector2i> p_path, int p_terrain_set, int p_terrain, bool p_ignore_empty_terrains) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_cells_terrain_path, p_path, p_terrain_set, p_terrain, p_ignore_empty_terrains);
}
TileMapCell TileMap::get_cell(int p_layer, const Vector2i &p_coords, bool p_use_proxies) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, TileMapCell(), get_cell, p_coords, p_use_proxies);
}
Vector2i TileMap::get_coords_for_body_rid(RID p_physics_body) {