### Godot version

4.0 stable

### System information

Windows 10

### Issue description

Running .clear() on a TileMap with Scene tiles leaves the tiles in place, as though nothing happened.

This appears to be the same issue as raised in [#69596](https://github.com/godotengine/godot/issues/69596), [#72456](https://github.com/godotengine/godot/pull/72456), and [67330](https://github.com/godotengine/godot/pull/67330). None of the previous issues seem to have presented a fix for this issue besides running some dummy operations on the TileMap, which have not had any effect for me.

Manually running queue_free() on each tile scene doesn't work, presumably since they are being cached. And running a dummy operation on the TileMap doesn't have any impact to speak of.

Not sure how to proceed, or if it's just impossible to remove Scene tiles once they're created.

### Steps to reproduce

The minimal reproduction project has a TileMap with several simple scene tiles. The attached script attempts to .clear() the TileMap when the user presses Enter, demonstrating my issue.

### Minimal reproduction project

[TileMapMinimumRecreationProject.zip](https://github.com/godotengine/godot/files/10959111/TileMapMinimumRecreationProject.zip)

if (pending_update || !is_inside_tree()) {
		return;
	}
	pending_update = true;
	call_deferred(SNAME("_update_dirty_quadrants"));
}
void TileMap::_update_dirty_quadrants() {
	if (!pending_update) {
		return;
	}
	if (!is_inside_tree() || !tile_set.is_valid()) {
		pending_update = false;
		return;
	}
	
	Transform2D gl_transform = get_global_transform();
	last_valid_transform = gl_transform;
	new_transform = gl_transform;
	
	for (Ref<TileMapLayer> &layer : layers) {
		layer->update_dirty_quadrants();
	}
	pending_update = false;
}
void TileMap::set_tileset(const Ref<TileSet> &p_tileset) {