### 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 (Ref<TileMapLayer> &layer : layers) {
		layer->clear_internals();
	}
}
void TileMap::_recreate_internals() {
	for (Ref<TileMapLayer> &layer : layers) {
		layer->recreate_internals();
	}
}
void TileMap::set_cell(int p_layer, const Vector2i &p_coords, int p_source_id, const Vector2i p_atlas_coords, int p_alternative_tile) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_cell, p_coords, p_source_id, p_atlas_coords, p_alternative_tile);
}
void TileMap::erase_cell(int p_layer, const Vector2i &p_coords) {
	TILEMAP_CALL_FOR_LAYER(p_layer, set_cell, p_coords, TileSet::INVALID_SOURCE, TileSetSource::INVALID_ATLAS_COORDS, TileSetSource::INVALID_TILE_ALTERNATIVE);
}
int TileMap::get_cell_source_id(int p_layer, const Vector2i &p_coords, bool p_use_proxies) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, TileSet::INVALID_SOURCE, get_cell_source_id, p_coords, p_use_proxies);
}
Vector2i TileMap::get_cell_atlas_coords(int p_layer, const Vector2i &p_coords, bool p_use_proxies) const {
	TILEMAP_CALL_FOR_LAYER_V(p_layer, TileSetSource::INVALID_ATLAS_COORDS, get_cell_atlas_coords, p_coords, p_use_proxies);
}
int TileMap::get_cell_alternative_tile(int p_layer, const Vector2i &p_coords, bool p_use_proxies) const {