### 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)

for (const Ref<TileMapLayer> &layer : layers) {
		if (layer->has_body_rid(p_physics_body)) {
			return layer->get_coords_for_body_rid(p_physics_body);
		}
	}
	ERR_FAIL_V_MSG(Vector2i(), vformat("No tiles for the given body RID %d.", p_physics_body.get_id()));
}
int TileMap::get_layer_for_body_rid(RID p_physics_body) {
	for (unsigned int i = 0; i < layers.size(); i++) {
		if (layers[i]->has_body_rid(p_physics_body)) {
			return i;
		}
	}
	ERR_FAIL_V_MSG(-1, vformat("No tiles for the given body RID %d.", p_physics_body.get_id()));
}
void TileMap::fix_invalid_tiles() {
	for (Ref<TileMapLayer> &layer : layers) {
		layer->fix_invalid_tiles();
	}
}
void TileMap::clear_layer(int p_layer) {
	TILEMAP_CALL_FOR_LAYER(p_layer, clear)
}
void TileMap::clear() {
	for (Ref<TileMapLayer> &layer : layers) {
		layer->clear();
	}
}
void TileMap::force_update(int p_layer) {